Cartridge assembly

ABSTRACT

A cartridge assembly comprises a housing having an illumination chamber and a well plate. The well plate is maintained within the housing and has liquid wells to receive desired amounts of liquids. The well plate includes a fluidics analysis station aligned with the illumination chamber, and an interface window and interface ports located at the fluidics analysis station. The well plate includes a valve station and pump station. A piercer unit is provided in the housing and positioned proximate to the wells. The piercer unit includes a piercer element and is to be moved to a piercing position where the piercer element pierces a cover for the corresponding well. A pump assembly on the well plate at the pump station manages fluid flow through the channels between the pump station and the fluidics analysis station. The housing includes a flow cell chamber to receive a removable flow cell cartridge.

RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.16/443,727, filed on Jun. 17, 2019, which is a continuation of U.S.application Ser. No. 15/729,729, filed on Oct. 11, 2017, which claimspriority from U.S. Provisional Application Ser. No. 62/408,631, filedOct. 14, 2016, and Dutch Application Serial No. 2017959, filed Dec. 8,2016, the content of each of which is incorporated by reference hereinin their entireties and for all purposes.

BACKGROUND

Various protocols used for biological or chemical research include theexecution of a large number of controlled reactions. The reactions maybe carried out in accordance with a predetermined protocol by automatedsystems that have, for example, suitable fluidics, optics, andelectronics. The systems may be used, for example, to generate abiological or chemical product for subsequent use or to analyze a sampleto detect certain properties/characteristics of the sample. Whenanalyzing a sample in some cases, a chemical moiety that includes anidentifiable label (e.g., fluorescent label) may be delivered to achamber where the sample is located and selectively bind to anotherchemical moiety of the sample. These chemical reactions may be observedor confirmed by exciting the labels with radiation and detecting lightemissions from the labels. Such light emissions may also be providedthrough other means, such as chemiluminescence.

Some known systems use a fluidic device, such as a flowcell, thatincludes a flow channel (e.g., interior chamber) defined by one or moreinterior surfaces of the flowcell. The reactions may be carried outalong the interior surfaces. The flowcell is typically positionedproximate to an optical assembly that includes a device for imaging thesample within the flow channel. The optical assembly may include anobjective lens and/or a solid state imaging device (e.g., CCD or CMOS).In some cases, an objective lens is not used and the solid state imagingdevice is positioned immediately adjacent to the flowcell for imagingthe flow channel.

Before imaging the flow channel, it may be necessary to conduct a numberof reactions with the sample. For example, in onesequencing-by-synthesis (SBS) technique, one or more surfaces of theflow channel have arrays of nucleic acid clusters (e.g., clonalamplicons) that are formed through bridge PCR. After generating theclusters, the nucleic acids are “linearized” to provide single strandedDNA (sstDNA). To complete a cycle of sequencing, a number of reactioncomponents are flowed into the flow channel according to a predeterminedschedule. For example, each sequencing cycle includes flowing one ormore nucleotides (e.g., A, T, G, C) into the flow channel for extendingthe sstDNA by a single base. A reversible terminator attached to thenucleotides may ensure that only a single nucleotide is incorporated bythe sstDNA per cycle. Each nucleotide has a unique fluorescent labelthat emits a color when excited (e.g., red, green, blue, and the like)that is used to detect the corresponding nucleotide. With thenewly-incorporated nucleotides, an image of numerous clusters is takenin four channels (i.e., one for each fluorescent label). After imaging,another reaction component is flowed into the flow channel to chemicallycleave the fluorescent label and the reversible terminator from thesstDNA. The sstDNA is then ready for another cycle. Accordingly, anumber of different reaction components are provided to the flow channelfor each cycle. A single sequencing session may include numerous cycles,such as 100, 300, or more.

The fluids that include the reaction components are typically held in astorage device (e.g., tray or cartridge) in which different fluids arestored in different reservoirs. Due to the number of reaction componentsand the large number of cycles, the total volume of fluid that is usedduring one session can be quite large. In fact, for some applications,it is impractical to supply the total volume of reaction components in asingle cartridge. For such applications, it may be necessary to use alarger system, multiple systems, or to execute numerous sessions with asingle system. These solutions can be costly, inconvenient, orunreasonable in some circumstances.

Definitions

All literature and similar material cited in this application,including, but not limited to, patents, patent applications, articles,books, treatises, and web pages, regardless of the format of suchliterature and similar materials, are expressly incorporated byreference in their entirety. In the event that one or more of theincorporated literature and similar materials differs from orcontradicts this application, including but not limited to definedterms, term usage, described techniques, or the like, this applicationcontrols.

As used herein, the following terms have the meanings indicated.

Examples described herein include various systems, methods, assemblies,and apparatuses used to detect desired reactions in a sample forbiological or chemical analysis. In some examples, the desired reactionsprovide optical signals that are detected by an optical assembly. Theoptical signals may be light emissions from labels or may betransmission light that has been reflected or refracted by the sample.For example, examples may be used to perform or facilitate performing asequencing protocol in which sstDNA is sequenced in a flow cell. Inparticular examples, the examples described herein can also perform anamplification protocol to generate a sample-of-interest for sequencing.

Examples herein enable desired reactions to occur where the desiredreactions include a change in at least one of a chemical, electrical,physical, and optical property or quality of a substance that is inresponse to a stimulus. For example, the desired reaction may be achemical transformation, chemical change, or chemical interaction. Inparticular examples, the desired reactions are detected by an imagingsystem. The imaging system may include an optical assembly that directsoptical signals to a sensor (e.g., CCD or CMOS). However, in otherexamples, the imaging system may detect the optical signals directly.For example, a flow cell may be mounted onto a CMOS sensor. However, thedesired reactions may also be a change in electrical properties. Forexample, the desired reaction may be a change in ion concentrationwithin a solution.

Exemplary reactions include, but are not limited to, chemical reactionssuch as reduction, oxidation, addition, elimination, rearrangement,esterification, amidation, etherification, cyclization, or substitution;binding interactions in which a first chemical binds to a secondchemical; dissociation reactions in which two or more chemicals detachfrom each other; fluorescence; luminescence; chemiluminescence; andbiological reactions, such as nucleic acid replication, nucleic acidamplification, nucleic acid hybridization, nucleic acid ligation,phosphorylation, enzymatic catalysis, receptor binding, or ligandbinding. The desired reaction can also be addition or elimination of aproton, for example, detectable as a change in pH of a surroundingsolution or environment.

Various examples include providing a reaction component to a sample. Asused herein, a “reaction component” or “reactant” includes any substancethat may be used to obtain a desired reaction. For example, reactioncomponents include reagents, enzymes, samples, other biomolecules, andbuffer solutions. The reaction components are typically delivered to areaction site (e.g., area where the sample is located) in a solution orimmobilized within a reaction site. The reaction components may interactdirectly or indirectly with the substance of interest.

In particular examples, the desired reactions are detected opticallythrough an optical assembly. The optical assembly may include an opticaltrain of optical components that cooperate with one another to directthe optical signals to an imaging device (e.g., CCD, CMOS, orphotomultiplier tubes). However, in alternative examples, the sampleregion may be positioned immediately adjacent to an activity detectorthat detects the desired reactions without the use of an optical train.The activity detector may be able detect predetermined events,properties, qualities, or characteristics within a predefined volume orarea. For example, an activity detector may be able to capture an imageof the predefined volume or area. An activity detector may be abledetect an ion concentration within a predefined volume of a solution oralong a predefined area. Exemplary activity detectors includecharged-coupled devices (COD's) (e.g., CCD cameras); photomultipliertubes (PMT's); molecular characterization devices or detectors, such asthose used with nanopores; microcircuit arrangements, such as thosedescribed in U.S. Pat. No. 7,595,883, which is incorporated herein byreference in the entirety; and CMOS-fabricated sensors having fieldeffect transistors (FET's), including chemically sensitive field effecttransistors (chemFET), ion-sensitive field effect transistors (ISFET),and/or metal oxide semiconductor field effect transistors (MOSFET).

As used herein, the term “illumination element” and “optical components”includes various elements that affect the propagation of opticalsignals. For example, the optical components may at least one ofredirect, filter, shape, magnify, or concentrate the optical signals.The optical signals that may be affected include the optical signalsthat are upstream from the sample and the optical signals that aredownstream from the sample. In a fluorescence-detection system, upstreamcomponents include those that direct excitation radiation toward thesample and downstream components include those that direct emissionradiation away from the sample. Optical components may be, for example,reflectors, dichroics, beam splitters, collimators, lenses, filters,wedges, prisms, mirrors, detectors, and the like. Optical componentsalso include bandpass filters, optical wedges, and optical devicessimilar to those described herein.

As used herein, the term “optical signals” or “light signals” includeselectromagnetic energy capable of being detected. The term includeslight emissions from labeled biological or chemical substances and alsoincludes transmitted light that is refracted or reflected by opticalsubstrates. Optical or light signals, including excitation radiationthat is incident upon the sample and light emissions that are providedby the sample, may have one or more spectral patterns. For example, morethan one type of label may be excited in an imaging session. In suchcases, the different types of labels may be excited by a commonexcitation light source or may be excited by different excitation lightsources at different times or at the same time. Each type of label mayemit optical signals having a spectral pattern that is different fromthe spectral pattern of other labels. For example, the spectral patternsmay have different emission spectra. The light emissions may be filteredto separately detect the optical signals from other emission spectra.

The illumination element and/or optical components may have fixedpositions in the optical assembly or may be selectively moveable. Asused herein, when the term “selectively” is used in conjunction with“moving” and similar terms, the phrase means that the position of theoptical component may be changed in a desired manner. At least one ofthe locations and the orientation of the optical component may bechanged. For example, in particular examples, a rotatable mirror isselectively moved to facilitate focusing an optical imaging system.

Analysis operations (also referred to as imaging sessions) include atime period in which at least a portion of the sample is imaged. Onesample may undergo or be subject to multiple imaging sessions. Forexample, one sample may be subject to two different imaging sessions inwhich each imaging session attempts to detect optical signals from oneor more different labels. As a specific example, a first scan along atleast a portion of a nucleic acid sample may detect labels associatedwith nucleotides A and C and a second scan along at least a portion ofthe sample may detect labels associated with nucleotides G and T. Insequencing examples, separate sessions can occur in separate cycles of asequencing protocol. Each cycle can include one or more imaging session.In other examples, detecting optical signals in different imagingsessions may include scanning different samples. Different samples maybe of the same type (e.g., two microarray chips) or of different types(e.g., a flow cell and a microarray chip).

During an analysis operation, optical signals provided by the sample areobserved. Various types of imaging may be used with examples describedherein. For example, examples described herein may utilize a “step andshoot” procedure in which regions of a sample area are individuallyimaged. Examples may also be configured to perform at least one ofepi-fluorescent imaging and total-internal-reflectance-fluorescence(TIRF) imaging. In other examples, the sample imager is a scanningtime-delay integration (TDI) system. Furthermore, the imaging sessionsmay include “line scanning” one or more samples such that a linear focalregion of light is scanned across the sample(s). Some methods of linescanning are described, for example, in U.S. Pat. No. 7,329,860 and U.S.Pat. Pub. No. 2009/0272914, each of which the complete subject matter isincorporated herein by reference in their entirety. Imaging sessions mayalso include moving a point focal region of light in a raster patternacross the sample(s). In alternative examples, imaging sessions mayinclude detecting light emissions that are generated, withoutillumination, and based entirely on emission properties of a labelwithin the sample (e.g., a radioactive or chemiluminescent component inthe sample). In alternative examples, flow cells may be mounted onto animager (e.g., CCD or CMOS) that detects the desired reactions.

As used herein, the term “sample” or “sample-of-interest” includesvarious materials or substances of interest that undergo an imagingsession where optical signals from the material or substance areobserved. In particular examples, a sample may include biological orchemical substances of interests and, optionally, an optical substrateor support structure that supports the biological or chemicalsubstances. As such, a sample may or may not include an opticalsubstrate or support structure. As used herein, the term “biological orchemical substances” may include a variety of biological or chemicalsubstances that are suitable for being imaged or examined with theoptical systems described herein. For example, biological or chemicalsubstances include biomolecules, such as nucleosides, nucleic acids,polynucleotides, oligonucleotides, proteins, enzymes, polypeptides,antibodies, antigens, ligands, receptors, polysaccharides,carbohydrates, polyphosphates, nanopores, organelles, lipid layers,cells, tissues, organisms, and biologically active chemical compound(s)such as analogs or mimetics of the aforementioned species. Otherchemical substances include labels that can be used for identification,examples of which include fluorescent labels and others set forth infurther detail below.

Different types of samples may include different optical substrates orsupport structures that affect incident light in different manners. Inparticular examples, samples to be detected can be attached to one ormore surfaces of a substrate or support structure. For example, flowcells may include one or more flow channels. In flow cells, the flowchannels may be separated from the surrounding environment by top andbottom layers of the flow cell. Thus, optical signals to be detected areprojected from within the support structure and may transmit throughmultiple layers of material having different refractive indices. Forexample, when detecting optical signals from an inner bottom surface ofa flow channel and when detecting optical signals from above the flowchannel, the optical signals that are desired to be detected maypropagate through a fluid having an index of refraction, through one ormore layers of the flow cells having different indices of refraction,and through the ambient environment having a different index ofrefraction.

The systems and methods set forth herein can be used to detect thepresence of a particular target molecule in a sample contacted with themicroarray. This can be determined, for example, based on binding of alabeled target analyte to a particular probe of the microarray or due toa target-dependent modification of a particular probe to incorporate,remove, or alter a label at the probe location. Any one of severalassays can be used to identify or characterize targets using amicroarray as described, for example, in U.S. Patent ApplicationPublication Nos. 2003/0108867; 2003/0108900; 2003/0170684; 2003/0207295;or 2005/0181394, each of which is hereby incorporated by reference.

Furthermore, optical systems described herein may be constructed toinclude various components and assemblies as described in PCTapplication PCT/US07/07991, entitled “System and Devices for Sequence bySynthesis Analysis”, filed Mar. 30, 2007 and/or to include variouscomponents and assemblies as described in International Publication No.WO 2009/042862, entitled “Fluorescence Excitation and Detection Systemand Method”, filed Sep. 26, 2008, both of which the complete subjectmatter are incorporated herein by reference in their entirety. Inparticular examples, optical systems can include various components andassemblies as described in U.S. Pat. No. 7,329,860 and WO 2009/137435,of which the complete subject matter is incorporated herein by referencein their entirety. Optical systems can also include various componentsand assemblies as described in U.S. patent application Ser. No.12/638,770, filed on Dec. 15, 2009, of which the complete subject matteris incorporated herein by reference in its entirety.

In particular examples, methods, and optical systems described hereinmay be used for sequencing nucleic acids. For example,sequencing-by-synthesis (SBS) protocols are particularly applicable. InSBS, pluralities of fluorescently labeled modified nucleotides are usedto sequence a plurality of clusters of amplified DNA (possibly millionsof clusters) present on the surface of an optical substrate (e.g., asurface that at least partially defines a channel in a flow cell). Theflow cells may contain nucleic acid samples for sequencing where theflow cells are placed within the appropriate flow cell holders. Thesamples for sequencing can take the form of single nucleic acidmolecules that are separated from each other so as to be individuallyresolvable, amplified populations of nucleic acid molecules in the formof clusters or other features, or beads that are attached to one or moremolecules of nucleic acid. Accordingly, sequencing can be carried out onan array such as those set forth previously herein. The nucleic acidscan be prepared such that they comprise an oligonucleotide primeradjacent to an unknown target sequence. To initiate the first SBSsequencing cycle, one or more differently labeled nucleotides, and DNApolymerase, etc., can be flowed into/through the flow cell by a fluidflow subsystem (not shown). Either a single type of nucleotide can beadded at a time, or the nucleotides used in the sequencing procedure canbe specially designed to possess a reversible termination property, thusallowing each cycle of the sequencing reaction to occur simultaneouslyin the presence of several types of labeled nucleotides (e.g. A, C, T,G). The nucleotides can include detectable label moieties such asfluorophores. Where the four nucleotides are mixed together, thepolymerase is able to select the correct base to incorporate and eachsequence is extended by a single base. Non-incorporated nucleotides canbe washed away by flowing a wash solution through the flow cell. One ormore lasers may excite the nucleic acids and induce fluorescence. Thefluorescence emitted from the nucleic acids is based upon thefluorophores of the incorporated base, and different fluorophores mayemit different wavelengths of emission light. A deblocking reagent canbe added to the flow cell to remove reversible terminator groups fromthe DNA strands that were extended and detected. The deblocking reagentcan then be washed away by flowing a wash solution through the flowcell. The flow cell is then ready for a further cycle of sequencingstarting with introduction of a labeled nucleotide as set forth above.The fluidic and detection steps can be repeated several times tocomplete a sequencing run. Exemplary sequencing methods are described,for example, in Bentley et al., Nature 456:53-59 (2008), WO 04/018497;U.S. Pat. No. 7,057,026; WO 91/06678; WO 07/123744; U.S. Pat. Nos.7,329,492; 7,211,414; 7,315,019; 7,405,281, and US 2008/0108082, each ofwhich is incorporated herein by reference.

In some examples, nucleic acids can be attached to a surface andamplified prior to or during sequencing. For example, amplification canbe carried out using bridge amplification to form nucleic acid clusterson a surface. Useful bridge amplification methods are described, forexample, in U.S. Pat. No. 5,641,658; U.S. Patent Publ. No. 2002/0055100;U.S. Pat. No. 7,115,400; U.S. Patent Publ. No. 2004/0096853; U.S. PatentPubl. No. 2004/0002090; U.S. Patent Publ. No. 2007/0128624; and U.S.Patent Publ. No. 2008/0009420. Another useful method for amplifyingnucleic acids on a surface is rolling circle amplification (RCA), forexample, as described in Lizardi et al., Nat. Genet. 19:225-232 (1998)and US 2007/0099208 A1, each of which is incorporated herein byreference. Emulsion PCR on beads can also be used, for example asdescribed in Dressman et al., Proc. Natl. Acad. Sci. USA 100:8817-8822(2003), WO 05/010145, or U.S. Patent Publ. Nos. 2005/0130173 or2005/0064460, each of which is incorporated herein by reference in itsentirety.

Other sequencing techniques that are applicable for use of the methodsand systems set forth herein are pyrosequencing, nanopore sequencing,and sequencing by ligation. Exemplary pyrosequencing techniques andsamples that are particularly useful are described in U.S. Pat. Nos.6,210,891; 6,258,568; 6,274,320 and Ronaghi, Genome Research 11:3-11(2001), each of which is incorporated herein by reference. Exemplarynanopore techniques and samples that are also useful are described inDeamer et al., Acc. Chem. Res. 35:817-825 (2002); Li et al., Nat. Mater.2:611-615 (2003); Soni et al., Clin Chem. 53:1996-2001 (2007) Healy etal., Nanomed. 2:459-481 (2007) and Cockroft et al., J. am. Chem. Soc.130:818-820; and U.S. Pat. No. 7,001,792, each of which is incorporatedherein by reference. In particular, these methods utilize repeated stepsof reagent delivery. An instrument or method set forth herein can beconfigured with reservoirs, valves, fluidic lines and other fluidiccomponents along with control systems for those components in order tointroduce reagents and detect optical signals according to a desiredprotocol such as those set forth in the references cited above. Any of avariety of samples can be used in these systems such as substrateshaving beads generated by emulsion PCR, substrates having zero-modewaveguides, substrates having integrated CMOS detectors, substrateshaving biological nanopores in lipid bilayers, solid-state substrateshaving synthetic nanopores, and others known in the art. Such samplesare described in the context of various sequencing techniques in thereferences cited above and further in US 2005/0042648; US 2005/0079510;US 2005/0130173; and WO 05/010145, each of which is incorporated hereinby reference.

Exemplary labels that can be detected in accordance with variousexamples, for example, when present on or within a support structureinclude, but are not limited to, a chromophore; luminophore;fluorophore; optically encoded nanoparticles; particles encoded with adiffraction-grating; electrochemiluminescent label such as Ru(bpy)32+;or moiety that can be detected based on an optical characteristic.Fluorophores that may be useful include, for example, fluorescentlanthanide complexes, including those of Europium and Terbium,fluorescein, rhodamine, tetramethylrhodamine, eosin, erythrosin,coumarin, methyl-coumarins, pyrene, Malacite green, Cy3, Cy5, stilbene,Lucifer Yellow, Cascade Blue™, Texas Red, alexa dyes, phycoerythin,bodipy, and others known in the art such as those described in Haugland,Molecular Probes Handbook, (Eugene, Oreg.) 6th Edition; The Synthegencatalog (Houston, Tex.), Lakowicz, Principles of FluorescenceSpectroscopy, 2nd Ed., Plenum Press New York (1999), or WO 98/59066,each of which is hereby incorporated by reference. In some examples, theone pair of labels may be excitable by a first excitation wavelength andanother pair of labels may be excitable by a second excitationwavelength.

Although examples are exemplified with regard to detection of samplesthat include biological or chemical substances supported by an opticalsubstrate, it will be understood that other samples can be imaged by theexamples described herein. Other exemplary samples include, but are notlimited to, biological specimens such as cells or tissues, electronicchips such as those used in computer processors, and the like. Examplesof some of the applications include microscopy, satellite scanners,high-resolution reprographics, fluorescent image acquisition, analyzingand sequencing of nucleic acids, DNA sequencing,sequencing-by-synthesis, imaging of microarrays, imaging ofholographically encoded micro-particles and the like.

SUMMARY

In accordance with examples herein, a cartridge assembly for use with afluidics analysis instrument is provided. The cartridge assemblycomprises housing, including a flow cell chamber to receive a flow cell,and a well plate having liquid wells to receive desired amounts ofliquids. The well plate includes a valve station, a pump station and afluidics analysis station. The well plate includes channels associatedwith the wells, the valve station, pump station and fluidics analysisstation. A pump assembly is provided on the well plate at the pumpstation. The pump assembly manages fluid flow through the channelsbetween the pump station and the fluidics analysis station. A rotaryvalve assembly is positioned on the well plate at the valve station. Therotary valve assembly includes a rotor shaft and rotor valve positionedto rotate about a rotational axis and to selectively couple the wells tothe pump station. The rotor shaft has a distal end exposed through thehousing. The rotor shaft includes a dual spline configuration at thedistal end thereof. The dual spline configuration has first and secondsets of splines. The first set of splines forms a drive interface andthe second set of splines forms a position encoding interface. Theposition encoding interface is utilized by the valve drive assembly totrack a position of the rotor shaft.

Optionally, the first set of splines represent exterior splinesextending about an exterior of the distal end, wherein lateral sides ofadjacent splines are separated by a first predetermined spline to splinespacing. The spline to spline spacing corresponds to a spline pattern ona drive shaft of a valve drive assembly. The second set of splines mayrepresent interior splines formed about an interior of a cavity providedat the distal end of the rotor shaft. The interior splines may havelateral sides that are angled such that adjacent lateral sides form apredetermined non-parallel angle with respect to one another. Theadjacent lateral sides may merge at a bottom to form pockets to receivemating splines on a drive shaft of the valve drive assembly.

Optionally, the rotor valve may be mounted to a proximal end of therotor shaft through a coupling flange. The coupling flange may allow apredetermined amount of tilting movement between the rotor valve androtor shaft. The rotor valve may include a rotor base having one or moreribs positioned about a proximal end of the rotor shaft. The couplingflange may be held between the ribs and the proximal end of the rotorshaft. The rotor valve may include well plate engaging face having acentral port and a radial port. The rotor valve may include a channeloriented to extend in a radial direction outward from the central portto the radial port.

Optionally, the central port may be aligned to correspond with arotational axis of the rotor shaft and align with a central feed port inthe well plate. The rotor valve may rotate about the rotational axis toalign the radial port with a corresponding well port. The rotary valvemay include a well plate engaging face formed with an interface ringthereon. The interface ring may extend about a perimeter of the wellplate engaging face. The cartridge assembly may further comprise a valvecap including an interior cavity to rotatably receive the rotary valve.The valve cap may include one or more latch arms to secure the valve capto the wells and downward against the well plate. A biasing element maybe within the interior cavity and may apply a biasing force against therotary valve to maintain a sealed interface between ports in the rotaryvalve and ports in the well plate.

Optionally, the pump assembly may include a plunger having a drive endand a biasing surface located at opposite ends of the plunger. The driveend and biasing surface may be exposed at upper and lower surfaces ofthe housing such that corresponding unidirectional drive and biasingforces are applied thereto in connection with moving the plunger in areciprocating motion. The plunger may have a drive arm and a plunger armjoined with one another through a bridge segment in a U-shape and may beformed together in a monolithic structure. The drive and plunger armsmay be received within support posts located on the well plate. Theplunger may comprise a plunger arm and plunger element that are moldedtogether from different materials. The plunger element may be formed ona leading end of the plunger arm. The plunger element may move withinthe corresponding support post to form high and low pressure states atthe pumping station.

Optionally, the pump station may include a channel segment functionallydivided into a preparation segment, a discharge segment and a pump worksegment, all of which are formed continuous with one another to supportfluid flow in either direction. The pump station may include a work areasandwiched between a pair of pinch valves located upstream anddownstream of the work area. The pump assembly may comprise a plungeraligned with the work area. The plunger may reciprocally move toward andaway from the work area to introduce high and low pressure states. Thepump assembly may further comprise push pins aligned with the pinchvalves. The push pins may be alternately moved to open and close thepinch valves. A piercer unit may be provided in the housing andpositioned proximate to the wells. The piercer unit may include apiercer element. The piercer unit may be moved to a piercing positionwhere the piercer element pierces a cover for the corresponding well.

Optionally, the housing may include a cover having a piercer accessopening that provides an instrument access to an upper end of thepiercer unit. The piercer unit may include a body that is shaped in aconical tubular manner with a lower platform, an intermediate segmentand an upper flange, at least one of the lower platforms or upper flangeincluding piercing elements distributed in a predetermined manner. Thepiercing elements may be arranged to align with the wells on the wellplate. A piercer unit may have a platform that fits over the rotorshaft. The platform may include indexing features that engage matingfeatures on the rotary valve assembly to locate the piercer unit in apredetermined rotational orientation with respect to the rotor shaft inorder to align piercer elements with corresponding wells.

Optionally, the well plate may include well transition ports arranged ina predetermined pattern corresponding to the rotary valve assembly. Thewell plate may include well discharge ports aligned with correspondingwells. The well plate may include well discharge channels extendingbetween corresponding well discharge ports and well transition ports.The well plate may include a base having top and bottom surfaces, atleast one of which includes the channels. The channels may include opensided channels. The base may be joined to a backing layer to close theopen sided channels. The well plate may include an optical interfacewindow, provided within the optical analysis station. A top side of thewell plate may include an insertion limit element to engage anillumination element on an instrument. The insertion limit element mayrepresent one or more ribs that are provided about the optical interfacewindow. The ribs may define a Z-tolerance between an illuminationelement and the optical interface window.

In accordance with examples herein, a fluidics system is providedcomprising a cartridge assembly that has a housing that includes anillumination chamber and a well plate. The well plate is maintainedwithin the housing and has liquid wells to receive desired amounts ofliquids. The well plate includes a fluidics analysis station alignedwith the illumination chamber. The well plate includes an interfacewindow and interface ports located at the fluidics analysis station. Aflow cell cartridge has a frame that contains an analysis circuittherein. The frame includes a flow cell window aligned with the analysiscircuit. The frame includes flow cell ports that are fluidly coupled toan active area in the analysis circuit. The housing includes a flow cellchamber to receive the flow cell cartridge. The flow cell chamber toposition the flow cell cartridge at the fluidics analysis station withthe flow cell window and ports aligned with the corresponding interfacewindow and ports, respectively.

Optionally, the flow cell chamber may include side rails and end stop,at least one of which has an end limit to position the flow cellcartridge, when in a fully loaded position, at a predetermined datumpoint such that the flow cell window and ports aligned with thecorresponding interface window and ports, respectively. The flow cellchamber may include a biasing arm that may be oriented to extend alongat least one of the side rails. The biasing arm may extend inward towardthe flow cell chamber and to apply a lateral biasing force upon the flowcell cartridge to maintain the flow cell cartridge at the predetermineddatum point. The biasing arm may include a latch element positioned tofit with a notch provided in a lateral side of the flow cell cartridge.The latch element may maintain the flow cell cartridge at an X datumpoint relative to an XYZ coordinate system (as described herein).

Optionally, the flow cell cartridge may include top and bottom frames.The top frame may include the flow cell window and ports. The top framemay include a rib extending upward from the top frame by a predeterminedheight to define a Z datum point relative to an XYZ coordinate system.The flow cell cartridge may include gaskets formed in a monolithicmanner from an elastomer material. The well plate may include a valvestation, pump station and interface channels. The interface channels mayprovide a first fluidic path between the valve station and one of theinterface ports and a second fluidic path between the pump station andone of the interface ports. The illumination chamber may be oriented toextend along an illumination axis that may extend through the interfacewindow, flow cell window and the active area within the analysiscircuit.

BRIEF DESCRIPTIONS OF THE DRAWINGS

FIG. 1A illustrates a front top perspective view of a cartridge assemblyformed in accordance with an example herein.

FIG. 1B illustrates a bottom perspective view of the cartridge assemblyof FIG. 1A in accordance with an example herein.

FIG. 1C illustrates a front perspective view of internal componentswithin the cartridge assembly in accordance with an example herein.

FIG. 1D illustrates a top perspective view of a waste tray that ismounted below the well plate and forms part of the housing of thecartridge assembly in accordance with examples herein.

FIG. 1E illustrates a front perspective view of a portion of thecartridge assembly and a flow cell cartridge align with the flow cellchamber in accordance with examples herein.

FIG. 1F illustrates a bottom plan view of the flow cell chamber with aflow cell cartridge inserted therein in accordance with an exampleherein.

FIG. 2A illustrates a perspective view of a rotary valve assembly formedin accordance with an example herein.

FIG. 2B illustrates an enlarged perspective view of the distal end ofthe rotor shaft in accordance with examples herein.

FIG. 2C illustrates a side sectional view of the rotary valve assemblywhich includes the valve shaft in accordance with examples herein.

FIG. 2D illustrates a top perspective view of the rotor valve formed inaccordance with an example herein.

FIG. 2E illustrates a bottom plan view of the rotor valve formed inaccordance with an example herein.

FIG. 2F illustrates a side perspective view of the rotor shaft and rotorvalve with the rotor cap removed in accordance with an example herein.

FIG. 3A illustrates a bottom perspective view of the piercer unit formedin accordance with an example herein

FIG. 3B illustrates a top view of a portion of the piercing unit wheninstalled on the rotary valve assembly in accordance with an exampleherein.

FIG. 3C illustrates the rotary valve assembly with the piercing unitremoved to better illustrate the valve shaft in accordance with anexample herein.

FIG. 4A illustrates a bottom view of a portion of the cartridge assemblyto illustrate the illumination chamber in more detail in accordance withexamples herein.

FIG. 4B illustrates a model side sectional view through the variousstructures provided at the fluidics analysis station once a flow cellcartridge is inserted and an illumination element is inserted into theillumination chamber in accordance with an example herein.

FIG. 5A illustrates a front perspective view of the well plate formed inaccordance with an example herein.

FIG. 5B illustrates flow channels provided on the back surface of thebase of the well plate in accordance with an example herein.

FIG. 5C illustrates a bottom plan view of a portion of the base toprovide a more detailed view of the fluidics analysis station on theback surface of the well plate in accordance with examples herein.

FIG. 5D illustrates a top plan view of a front/top portion of the basecorresponding to FIG. 5C to provide a more detailed view of the fluidicsanalysis station on a front surface of the well plate in accordance withexamples herein.

FIG. 5E illustrates an enlarged portion of the bottom surface of thebase proximate to the valve station in accordance with examples herein.

FIG. 6A illustrates a top plan view of the pump station on the wellplate in accordance with an example herein.

FIG. 6B illustrates a side view of a plunger provided within the pump inaccordance with an example herein.

FIG. 6C illustrates an enlarged side view of the plunger element asmounted to the plunger arm in accordance with an example herein.

FIG. 6D illustrates a side sectional view of the pump station to betterillustrate the pumping operation in accordance with an example herein.

FIG. 6E illustrates an enlarged side perspective view of a portion ofthe plunger inserted into the support post in accordance with an exampleherein.

FIG. 6F illustrates a perspective view of the support shaft to receivethe plunger arm in accordance with examples herein.

FIG. 7 illustrates a block diagram of a portion of a fluidics instrumentutilized in accordance with an example herein.

FIG. 8 is a schematic view of a system configured for biological orchemical analysis formed in accordance with one example.

FIG. 9A illustrates a top perspective view of a flow cell cartridgeformed in accordance with an example herein.

FIG. 9B illustrates an enlarged view of a portion of the top frame tobetter illustrate an optical fluidic (O-F) interface to the flow cellcartridge in accordance with examples herein.

FIG. 9C illustrates a bottom perspective view of the flow cell cartridgeof FIG. 9A in accordance with examples herein.

FIG. 9D illustrates a top view of a portion of a printed circuit boardprovided within the flow cell cartridge formed in accordance with anexample herein.

FIG. 9E illustrates a bottom view of the printed circuit board of FIG.9D formed in accordance with an example herein.

DETAILED DESCRIPTION Cartridge Assembly Overview

FIG. 1A illustrates a front top perspective view of a cartridge assembly100 formed in accordance with an example herein. By way of example thecartridge assembly 100 may represent an SBS cartridge assembly. Thecartridge assembly 100 includes a housing to be inserted into amicro-fluidics instrument. While examples herein are described inconnection with micro-fluidics systems, instruments and cartridges,optionally examples may be implemented with fluidics systems that maynot otherwise be considered “micro” fluidics system, instruments,cartridges, etc. The housing includes a base 101 and a cover 102. Thecover 102 includes an instrument engaging surface 104 that includesopenings to expose internal components that are engaged by multipleinstrument components described below in more detail. During operation,the cartridge assembly 100 is positioned proximate to an instrument thatphysically, optically and electrically couples to the cartridge assembly100 in connection with performing a fluidics operation. The cartridgeassembly 100 includes a front face 106 that includes a flow cell chamber108 to receive a flow cell in connection with performing a fluidicsoperation.

In accordance with examples herein, the cartridge assembly 100 includesvarious subassemblies including a rotary valve assembly 200 (describedbelow in more detail in connection with FIGS. 2A-2D), a piercer unit 300(described below in more detail in connection with FIGS. 3A-3D), anillumination chamber 400 (described below in more detail in connectionwith FIG. 4 ), and a syringe pump assembly 500 (described below in moredetail in connection with FIGS. 6A-6C).

The cover 102 includes a shaft well 116 that exposes a valve shaftwithin the rotary valve assembly 200. The cover 102 also includespiercer access openings 122 that provide the instrument access to anupper end of the piercer unit 300 in connection with operationsdescribed herein. During operation, a drive shaft on the instrument isphysically coupled to the valve shaft of the rotary valve assembly 200to manage movement of the rotary valve assembly 200. The cover 102includes piercer access openings 122 that provide one or more piercershafts on the instrument access to an upper end of the piercer unit 300in connection with a well foil piercing operation. By way of example,multiple piercer access openings 122 may be provided in a distributedmanner across an upper end of the piercer unit 300 in order to maintainplanar motion of the piercer unit 300 when being activated. A samplewell 124 is provided proximate to the front face 106. The sample well124 is to receive a sample quantity of interest to be analyzed by theinstrument. A heating element 125 may be provided proximate to thesample well 124 to adjust the temperature of incoming samples as desired(e.g., to preheat). A pump access opening 123 is provided in the uppersurface 104 of the cover 102. The pump access opening 123 is to allow abiasing element within the instrument to engage a spring engagingsurface 542 on a plunger of the pump assembly 500. For example, thebiasing element may be a metal wave spring, an elastomeric spring, oranother structure that provides a uniform force.

FIG. 1B illustrates a bottom perspective view of the cartridge assembly100 of FIG. 1A. In FIG. 1B, a flow cell cartridge 900 is provided withinthe flow cell chamber 108. The cartridge assembly 100 includes a bottomsurface 110 having a flow cell cartridge access area 112 that exposesportions of interest on the flow cell cartridge 900, such as an array ofelectrical contact pads 950 and an opening 944 to receive a heaterelement. The bottom surface 110 also includes a pair of pushpin openings114 and a pump drive opening 116. The pushpin openings 114 exposepushpins within the pump 500. As explained herein, the pushpins areengaged by valve drive shafts within the instrument to open and closecorresponding pinch valves in connection with managing fluid flow. Thepump drive opening 116 exposes a proximal end 548 of a valve shaft 546within the pump 500. As explained herein, the valve shaft 546 is engagedby a pump drive shaft within the instrument to introduce a pumpingaction in connection with managing fluid flow. The bottom surface 110also includes an opening 118 to expose a pierceable waste discharge port120 that is utilized to drain used fluids from a waste container withinthe cartridge assembly 100.

FIG. 1C illustrates a front perspective view of internal componentswithin the cartridge assembly 100 in accordance with an example herein.As shown in FIG. 1C, the cartridge assembly 100 includes a rotary valve200 assembly rotatably mounted onto a well plate 150 in a valveoperating station. A syringe pump assembly 500 is mounted onto the wellplate 150 in a pumping station. The well plate 150 includes a base 152(e.g., a generally planar later) with multiple reagent wells 154, 156formed with and extending upward from the base 152. The reagent wells154, 156 are provided at various positions at least partiallysurrounding the rotary valve assembly 200. The reagent wells are toreceive desired amounts of liquids. Optionally, the wells 154, 156 mayinclude samples and other liquids. As explained herein, the rotary valveassembly 200 selectively couples the reagent wells 154, 156 (generallyreferred to as liquid wells) to the fluidics analysis station 170.

The reagent wells 154, 156 may be formed with different cross-sectionalareas and have different heights extending above the base 152 to definedifferent well volumes to receive a desired quantity of liquid for thecorresponding reagent. Optionally, one or more of the wells 154, 156 maybe utilized as solution wells in accordance with examples herein. Thewells 154, 156 include filling ends 158, 160 that are open to receive adesired amount of liquid during a filling operation. Once the desiredamount of liquid is added to the wells 154, 156, the filling ends 158,160 are covered with a foil or other sealing cover to form an airtightvolume within each of the wells 154, 156. While not visible in FIG. 1C,the wells 154, 156 include one or more discharge ports provided in thebottom thereof. During operation, the cover is pierced to allow air toenter one or more of the well volumes, thereby permitting the liquid tofreely flow (e.g. through gravity or under pressure) through thedischarge ports to the fluidics analysis station 170 under control ofthe rotary valve 200 and pump assembly 500.

FIG. 1D illustrates a top perspective view of a waste tray 130 that ismounted below the well plate 150 and forms part of the housing of thecartridge assembly 100. The waste tray includes a waste collectionvolume 131 that spans an area below a relatively large portion of thewell plate 150. By way of example, the waste tray 130 is located belowthe rotary valve assembly 200 and at least a portion of the wells 154,156. The waste tray 130 includes a ridge 132 that extends about aperimeter thereof and is sealed to a mating surface (e.g. on the bottomsurface of the well plate 150). The ridge 132 may include vents 133 inthe corners thereof that communicate with openings through the wellplate 150. The vents 133 permit air to discharge from the volume 131 aswaste liquids enter the volume 131. The vents 133 are positioned abovethe area in which the liquid is retained to prevent leakage. The vents133 are distributed to allow the cartridge assembly 100 to be slightlytilted during operation such that at least one of the vents 133 willalways be usable as an air inlet. The vents 133 allow the size of thewaste tray 130 to be limited as waste liquids are permitted to slosh upto the surface of the vents 133 without leaking. The vents 133 may beformed of a porous material, such as expanded poly propylene,polyethylene or polytetrafluoroethylene.

The waste tray 130 also includes a funnel region 134 and a dischargetube 135. The funnel region 134 terminates at a ledge area 136 thatcommunicates with an opening to the tube 135. The bottom end of the tube135 is initially closed with a cover. To empty the waste tray 130, thecover 136 may be pierced and the cartridge assembly 100 (including thewaste tray 130) tilted with the funnel region 134 at the lowest pointtherein. The waste liquids flow through the funnel region 134 over theledge area 136 and out of the tube 135.

Flow Cell Chamber

FIG. 1E illustrates a front perspective view of a portion of thecartridge assembly 100 and a flow cell cartridge 900 align with the flowcell chamber 108. The flow cell chamber 108 includes a key feature 109which may be shaped as a channel and provided in the bottom surface ofthe flow cell chamber 108. The key feature 109 is shaped and dimensionedto receive a corresponding keying feature (e.g. standoff 914 FIG. 9C) ona bottom of the flow cell cartridge 900 to ensure that the flow cellcartridge 900 is loaded in the correct direction and orientation. Theflow cell chamber 108 includes side rails 413 and upper and lower walls451 and 453. The cartridge 900 is inserted in a loading direction 9A.

FIG. 1F illustrates a bottom plan view of the flow cell chamber 108 witha flow cell cartridge 900 inserted therein in accordance with an exampleherein. The flow cell cartridge 900 is inserted into the flow cellchamber 108 to a fully loaded position in FIG. 1F. As described herein,in more detail in connection with FIGS. 9A-9E, the flow cell cartridge900 includes a loading end 908 and lateral edges 912. The loading end908 includes a reference post 923, while at least one of the lateraledges 912 includes one or more lateral reference posts 925. An oppositelateral edge 912 includes a notch 927. A bottom side of the flow cellcartridge 900 includes openings to expose a heat spreader 957 andcontact pads 950.

The flow cell chamber 108 includes top and bottom surfaces, and lateralside rails 413 that extend parallel to one another along oppositelateral sides of the chamber 108. An end stop 417 is provided at aninnermost depth of the chamber 108. The top and bottom surfaces, lateralside rails 413, and end stop 417 are positioned to orient the flow cellcartridge 900 at predetermined datum points (e.g., reference pointsreferred to as an X datum point, Y datum point and Z datum point)relative to a coordinate system (e.g., XYZ coordinate system). The endstop 417 includes an end limiter 414 provided at a desired positionalong the end stop 417. The end limiter 414 aligns with a reference post923 provided on the loading end 908. One of the side rails 413 includeslateral limits 420 that extend inward towards the flow cell chamber 108.The lateral limits 420 align with the lateral reference post 923. Theopposite side rail 413 includes a biasing arm 422 that is oriented toextend along the side rail 413 and to apply a lateral biasing force inthe direction of arrow 1E. The biasing arm 422 includes a latch element424 on a distal end thereof. The latch element 424 is shaped to fit inthe notch 927 in the side edge 912.

During a loading operation, the loading end 908 is inserted into theflow cell chamber 108 until the reference post 923 firmly abuts againsta limit feature in the flow cell chamber 108 to define a limit ofmovement in the loading direction 9A. As flow cell cartridge 900 isinserted, the biasing arm 422 rides along the side edge 912 thatincludes the notch 927 until the latch element 424 fits within the notch927. The biasing arm 422 applies a lateral force in the direction ofarrow 1E (also represents a lateral positioning force) to shift the flowcell cartridge 900 in the lateral direction (corresponding to theY-axis) until the lateral reference posts 923 engage the lateral limits420. The lateral limits of the flow cell chamber 108 define a limit ofmovement in the lateral Y-direction. The biasing arm maintains the flowcell cartridge 900 at the desired Y-position (corresponding to a Y datumpoint). The latch element 424 within the notch 927 at a predefinedposition to maintain the flow cell cartridge 900 at the desiredX-position (corresponding to an X datum point).

The flow cell chamber 108 enables a snap-in arrangement for the flowcell cartridge 900. By enabling the flow cell cartridge 900 to beinserted into and removed from the cartridge assembly 100, examplesherein allow the flow cell cartridge to be managed and shippedseparately from the reagents and samples. In addition, by separating theflow cell cartridge 900 from the reagents, examples herein allowseparate manufacturing workflows. In addition, examples herein allowflow cell cartridges to be mixed and matched with various combinationsof reagents, reagent volumes and flow cell cartridge sizes. For example,one protocol may utilize larger volumes of certain reagents, whileanother protocol utilizes a greater number of different reagents, but insmaller volumes. The various criteria for the number and volume ofreagents may be satisfied by different cartridge assemblies, while anyof the foregoing cartridge assemblies are able to utilize the same flowcell cartridge. As a further example, the same type of cartridgeassembly may be utilized with different protocols that have differentrequirements within the analysis circuit. For example, one protocol mayutilize an analysis circuit that has a large optical footprint, whileanother protocol may utilize an analysis circuit that has a smalleroptical footprint. In addition, some protocols may utilize analysiscircuits that have more complex electronics and interconnections, ascompared to other analysis circuits, while any of the foregoing analysiscircuits may be embodied within a flow cell cartridge having a commonoverall envelope that fits into the same cartridge assembly.

Examples described herein provide an interface having a small height(e.g. a minimized height) between the analysis circuit and the lightsource within the illumination element of the instrument.

Piercer Unit

A piercer unit 300 is provided in the housing and positioned proximateto the wells 154, 156. The piercer unit 300 is moved to a piercingposition where piercer elements pierce a foil or cover for thecorresponding well(s) 154, 156. In the example of FIG. 3A, the piercerunit 300 is mounted on the rotary valve assembly 200 and is managedduring operation by the instrument to pierce one or more of the wells154, 156.

FIG. 3A illustrates a bottom perspective view of the piercer unit 300 isformed in accordance with an example herein. The piercer unit 300 isillustrated with a partial cut out to better present the overallstructure therein. The piercer unit 300 includes a body 306 that isshaped in a conical tubular manner with a lower platform 302, anintermediate segment 308 and an upper flange 310. The platform 302,segment 308, and flange 310 are formed in a monolithic manner. The lowerplatform 302 includes a plurality of piercing elements 312 distributedin a predetermined manner about the platform 302. In the example of FIG.3A, the piercing elements 312 are arranged in a circular pattern. Theupper flange 310 also includes piercing elements 314 provided on a lowersurface thereof and projecting in a common direction as the piercingelements 312. The piercing elements 314 are distributed about the upperflange 310 in a predetermined manner, such as in a circular pattern.

During operation, the piercing unit 300 is activated by a pierceractuator assembly on the instrument. For example, with reference to FIG.1A, the instrument may extend one or more piercer shafts through thepiercer access ports 122 in the cover 102. The piercer shafts pushdownward in a piercing direction 318 to force the piercing unit 300downward, thereby driving the piercing elements 312, 314 through thefoil/cover on the corresponding wells 154, 156. The piercer shafts aredistributed to evenly apply the piercing force to the piercer unit 300.

In accordance with at least one example, the piercing elements 312, 314are formed with an X-shaped cross-section to facilitate piercing thefoil/cover and to provide venting through the foil/cover. The X-shapedcross-section allows air to enter the corresponding well volume evenwhile the piercing elements 312, 314 extend through the foil/covers.

In the example of FIG. 3A, a majority the piercing elements 312, 314have a generally common length. However, optionally various ones of thepiercing elements 312, 314 may be longer or shorter, such as shown bypiercing element 314A. With joint reference to FIGS. 10 and 3A, thepiercing elements 312, 314 are positioned to align with correspondingwells 154, 156. In the example of FIGS. 10 and 3A, the piercing elements312, 314 generally have a common length to pierce each of thecorresponding wells 154, 156 at the same time when the piercing element300 is activated. Optionally, the piercing unit 300 may be operated (bythe piercer actuator assembly) as a multistage piercing system such thatonly a portion of the piercing elements 312, 314 pierce correspondingwells 154, 156 during a first piercing operation, while a differentportion of the piercing elements 312, 314 pierce corresponding wells154, 156 during a second piercing operation. For example, the piercingelements 312 may be formed longer than the piercing elements 314 suchthat the piercing elements 312 pierce corresponding foils during thefirst piercing operation, and the piercing elements 314 piercecorresponding foils during the second piercing operation.

The lower platform 302 includes an internal rim 326 that is formed aboutthe opening 304. The rim 326 includes multiple indexing features 322provided about the opening 304. The indexing features 322 engage matingfeatures on the rotary valve assembly 200 in order to locate the piercerunit 300 in a predetermined rotational orientation with respect to therotor shaft 202 in order to align the piercer elements 312, 314 withcorresponding wells 154, 156. The indexing features 322 include one ormore notches 324 which are provided about the internal rim 326. The rim326 projects slightly upward into an interior portion of the body 306toward the upper flange 310. The notches 324 are distributed in apredetermined pattern about the opening 304. The notches 324 align withribs or teeth that are provided on the rotary valve assembly 200 (asdescribed below in more detail). In the example of FIG. 3A, notches 324are relatively evenly positioned about the perimeter of the opening 304.Additionally or alternatively, more or fewer notches 324 may be utilizedand may be positioned in alternative locations in an even or unevendistribution. Optionally, an indexing feature other than notches 324 maybe utilized.

The rim 326 also includes one or more flexible standoff 328 that extenddownward into the opening 304 in a direction common with the piercingelements 312. The standoffs 328 engage a ledge 216A extending about aperimeter of the base extension 216. Once the notches 324 align withcorresponding teeth on the rotary valve assembly 200, the piercer unit300 is loaded until the standoffs 328 rest on a top surface of the ledge216A. The standoffs 328 remain on the ledge 216A to maintain thepiercing unit 300 positioned vertically in a non-piercing/readyposition. During operation, the piercer unit 300 is forced downward (inthe direction of arrow 318) by a piercer shaft, in response to which thestandoffs 328 flex outward and ride down over the ledge 216A to permitthe piercer unit 300 to slide downward in the piercing direction 318further onto the rotor cap 210.

FIG. 3B illustrates a top view of a portion of the piercing unit 300when installed on the rotary valve assembly 200. As explained herein,the rotary valve assembly 200 includes a rotor shaft 202 with a valvecap 210 mounted over the rotor shaft 202. The valve cap 210 includes aplurality of teeth 212 distributed peripherally about a central rim ofthe valve cap 210. The teeth 212 align with, and are received in, thenotches 324 on the piercer unit 300 in order to rotationally positionthe piercing unit 300 in a predetermined rotational angle relative tothe rotary valve assembly 200. While not shown, the latches 328 (FIG.3A) are securely joined with latching features on the valve cap 210 tomaintain the piercing unit 300 in a mounted position along a rotationalaxis extending along a central axis of the rotor shaft 202 of the rotaryvalve assembly 200.

FIG. 3C illustrates the rotary valve assembly 200 with the piercing unit300 removed to better illustrate the rotor shaft 202. The rotor shaft202 is elongated and rotates about a rotational axis 220. The rotorshaft 202 includes a proximal end (not visible in FIG. 3C) and a distalend 204. The valve cap 210 is loaded over the distal end 204 of therotor shaft 202 to an installed position as shown in FIG. 3C. The valvecap 210 includes a cap base 214 that has an enlarged diameter that isdimensioned to fit within a collection of wells 156 that are arrangedadjacent one another in a generally circular manner. The cap base 214 isjoined with a cap extension 216 that extends upward from the cap base214 along a length of the rotor shaft 202. The cap extension 216 has asmaller diameter than the diameter of the cap base 214 in the example ofFIG. 3C. However, it is recognized that alternative dimensions may beutilized for the cap extension 216 and cap base 214. The cap extension216 includes teeth 212 formed upon a periphery of the cap extension 216and projects outward radially (relative to the rotational axis 220)therefrom.

The cap base 214 includes one or more latch arms 226 that extendradially outward from the cap base 214. The latch arms 226 are formed inan L-shape and dimensioned such that a leg of the latch arm 226 fitsbetween adjacent wells 156, while an outer portion or foot on the latcharm 226 bends about and rests securely against an outer surface of oneof the wells 156. The corresponding well 156 includes a detent 158provided on an outer wall of the well 156. The L-shaped latch arm 226snaps over and is held securely below the detent 158 when the valve cap210 is inserted over the rotor shaft 202

Rotary Valve Assembly

Next, the operation of the rotary valve assembly 200 will be describedin connection with FIGS. 2A-2F.

FIG. 2A illustrates a perspective view of a rotary valve assembly 200formed in accordance with an example herein. FIG. 2A better illustratesthe valve cap 210 provided over the rotor shaft 202. The rotor shaft 202rotates within the valve cap 210, with the valve cap 210 maintaining therotor shaft 202 at a predetermined position with respect to the wellplate 150. The valve cap 210 includes multiple latch arms 226distributed evenly about a perimeter of the cap base 214. A distal end204 of the rotor shaft 202 projects beyond the cap extension 216. Thedistal end 204 includes a plurality of exterior splines 230 distributedabout the rotor shaft 202. The distal end 204 also includes a cavity 228that includes interior splines 232 distributed about the cavity 228. Therotor shaft 202 includes a dual spline configuration having the interiorand exterior splines 232, 230 (also referred to as first and second setsof splines) that mate with a matching spline configuration on a driveshaft of a valve drive assembly within the instrument that engages thecartridge assembly during a fluidics operation. The dual splineconfiguration of interior and exterior splines 232, 230 provides a driveinterface and a position encoding interface to precisely track arotational relation between the drive shaft of the instrument and therotor shaft 202.

The valve cap 210 is illustrated in a partially transparent manner toshow a rotor valve 234 below the valve cap 210 and mounted about aproximal end of the rotor shaft 202. The rotor valve 234 is secured tothe rotor shaft 202 and rotates with the rotor shaft 202. The rotorvalve 234 rotates within (and relative to) the cap base 214, while thecap base 214 remains stationary with the latch arms 226 secured aboutcorresponding wells on the well plate 150. An inner diameter of the capextension 216 corresponds to an outer diameter of the rotor shaft 202 toprovide a close tolerance there between. The cap extension 216 has alength 217 that may be varied, provided that the cap extension 216affords sufficient structural and rotational support to the rotor shaft202, whereby the rotational axis of the rotor shaft 202 is maintained ata predetermined fixed point relative to the well plate 150. By way ofexample, the rotational axis of the rotor shaft 202 may correspond witha central port provided in the well plate through which fluids travel.As explained herein, the valve drive assembly of the instrument rotatesthe rotor shaft 202, which in turn rotates the rotary valve 234 in orderto fluidly couple a desired one of the wells 154, 156 with the centralport below the rotor shaft 202.

FIG. 2B illustrates an enlarged perspective view of the distal end 204of the rotor shaft 202. The interior and exterior splines 232, 230 havedifferent spline shapes. The exterior splines 230 represent a first setof splines that form a drive interface, such that the first/exteriorsplines are engaged by mating splines of a driveshaft of a valve driveassembly. The interior splines 232 represent a second set of splinesthat form a position encoding interface that is utilized by the valvedrive assembly to maintain a fully mated (and closely tracked)interconnection between the driveshaft of the valve drive assembly andthe rotor shaft 202. The exterior splines 230 have spline lateral sides233 that extend substantially parallel to one another. The exteriorsplines 230 are oriented to extend substantially parallel to one anotherwith lateral sides 233 of adjacent splines separated by a firstpredetermined spline to spline spacing 231. The spline to spline spacing231 corresponds to a spline pattern on a drive shaft of a valve driveassembly. The spline displaying spacing 231 is defined to be slightlylarger than the mating splines from the shaft drive assembly in order tofacilitate engagement. By providing the spline to spline spacing 231larger than the incoming splines, a slight amount of slack is introducedthat may otherwise permit a limited amount of relative rotational shiftbetween the rotor shaft and the driveshaft. Accordingly, the splines ofthe driveshaft may not be an exact indicator of the rotational positionof the rotor shaft 230. Instead, the interior splines 232 form aposition encoding interface that is utilized to provide positionencoding information when joined with a separate positionencoding/tracking element of the drive assembly as explained herein. Theposition encoding interface is utilized by the valve drive assembly toclosely and precisely track a position of the rotor shaft independent ofthe drive splines the join the exterior splines 230. The interiorsplines 232 have lateral sides 235 that extend in a V-shape such thatadjacent lateral sides form a predetermined non-parallel angle 237 withrespect to one another (e.g., a 30 degree angle). The lateral sides 235merge at the bottom of the interior splines 232 to form V-shaped pocketsthat receive mating splines on the drive shaft of the valve driveassembly. The splines 232 fully engage the mating splines on the driveshaft and cooperate to avoid backlash. The splines 232 also allow thedrive shaft to operate at a somewhat “skewed” orientation or angle tothe rotor shaft 202. The splines 230, 232 and distal edge of the distalend may be configured with beveled edges to facilitate alignment of thedrive shaft and avoid the drive shaft from merely butting against adistal end of the rotor shaft 202 without the splines aligning.

The dual spline configuration of FIG. 2B utilizes the exterior splines230 to be relatively “loosely” engaged and driven by splines of thevalve drive assembly, while utilizing the interior splines 232 to berelatively “closely” engaged by a position encoder that monitors therotational position of the rotor shaft 202.

FIG. 2C illustrates a side sectional view of the rotary valve assembly200 which includes the rotor shaft 202, valve cap 210, and rotary valve234. FIG. 2B illustrates proximal and distal ends 203, 204 of the rotorshaft 202. The rotor shaft 202 is elongated and held in position by thevalve cap 210 to rotate about the rotational axis 220. FIG. 2Billustrates a cross-sectional envelope of the valve cap 210 whichillustrates the cap base 214 to have a greater diameter than the capextension 216. The cap extension 216 includes an interior passage 219having an inner diameter that substantially corresponds to the outerdiameter of the rotor shaft 202. The interior passage 219 of the capextension 216 holds the rotor shaft 202 in a predetermined orientationwith the rotational axis 220 centered at a desired point on the wellplate (e.g., corresponding to a central feed port).

FIG. 2D illustrates a top perspective view of the rotor valve 234 formedin accordance with an example herein. The rotor valve 234 includes arotor base 240 having an upper surface and a well plate engaging face238. The rotor base 240 may be injection molded with polypropylene oranother material with desired properties. A fluid channel 246 isprovided within the rotor base 240. The fluid channel 246 is oriented toextend in a radial direction outward from a central point of the rotorbase 240, corresponding to a central port 248. The fluid channel 246extends to a peripheral point on the rotor base 240 and terminates at aradial port 250. The central and radial ports 248, 250 extend throughthe rotor base 240 to open onto a well plate engaging face 238. Thecentral port 248 may be aligned to correspond with the rotational axis220 of the rotor shaft 202 and aligned with a central feed port in thewell plate 150. The rotor valve 234 is rotated about the rotational axis220 in either radial direction 252 to align the radial port 250 with acorresponding well transition port 162 in connection with pulling areagent or sample of interest from a well.

The upper surface of the rotor base 240 includes a recessed cavity 261surrounding the fluid channel 246. The recessed cavity 261 is shaped toreceive a channel cover 258 to cover an open face of the fluid channel246. The channel cover 258 extends a full length of the fluid channel246 to entirely enclose the fluid channel 246. The channel cover 258 maybe laser bonded or otherwise joined to the rotor base 240. In thepresent example, an open faced fluid channel 246 and channel cover 258are utilized to afford an easy and reliable manufacturing process.Optionally, alternative structures may be utilized to provide the fluidchannel, while eliminating the channel cover 258, such as by forming afluid channel within the monolithic structure of the rotor base 240,thereby avoiding the need to provide the channel cover 258.

The upper surface of the rotor base 240 has a peripheral rib 242 and aninterior rib 256 which extend upward from the rotor base 240. The wellplate mating face 238 faces in a direction opposite to the peripheraland interior ribs 242, 256. A biasing element 253 (e.g., a wave springor other structure) is provided within the interior cavity 213 andapplies a biasing force against the rotary valve 234. The biasingelement 253 is located on the rotor base 240 about the interior rib 256.The biasing element 253 applies an expansion force against the rotorbase 240 and the valve cap 210 to maintain a sealed interface betweenthe ports 248, 250 on the rotor valve 234 and ports on the well plate150.

FIG. 2E illustrates a bottom plan view of the rotor base 240. The wellplate engaging face 238 is formed by an interface ring 260 and aninterface pad 262. The interface ring 260 extends about a perimeter ofthe rotor base 240. With reference to FIG. 2C, the interface pad 262 inthe interface ring 260 form a slight standoff to maintain the rotor base240 off of the well plate 150. In one example, the interface ring 260may be formed with a smooth flat lower surface. In another example, theinterface ring 260 may be formed with a predetermined pattern formed onthe outer surface of the interface ring 260 in order to reduce thecontact area between the interface pad 260 and the well plate 150. Forexample, the pattern may comprise a collection of inter-connectedcircular or O-ring shaped features formed on the interface ring 260(e.g., in a chain pattern). For example, detail 2E is illustrated withan alternative configuration for the surface of the interface ring 260.At detail 2E, the interface ring 260A is provided with a series ofcircular raised rings/portions 261A that surround recesses 262A. Forexample, the pattern in detail 2E may resemble a chain or series ofadjoining eights, although alternative patterns maybe used. When not inuse, the interface ring 260A may be rotated to a position at which therecesses 262A align with the ports in the well plate to avoid creep inthe port structure.

The rotor base 240, interface ring 260 and interface pad 262 may beformed from a multi-shot (e.g. two shot) molding process with the rotorbase formed of one type of material, while the interface ring 260 andinterface pad 262 are formed of another type of material. For example,the interface pad 262 and the interface ring 260 may be formed from athermoplastic elastomer (TPE) or other similar materials. The radialport 250 extends through the interface ring 260. The interface pad 262is formed about the central port 248. The central port 248 is positionedto align with the central feed port 161 on the well plate 150, while theradial port 250 is rotated to align with different well transition ports162. The central interface pad 262 and interface ring 260 are formedduring a common injection molding operation by injecting a thermoplasticelastomer at one or more gates. The radial port 250 may be formed as anoval with an elongated dimension extending along an arc (relative to thecentral port 248) about the interface ring 260. The oval shape of radialport 250 affords a predetermined amount of tolerance when aligning witha mating well port.

FIG. 2F illustrates a side perspective view of the rotor shaft 202 androtor valve 234 (with the rotor 210 removed). FIG. 2F illustrates therotor shaft 202 extending along the rotational axis 220. The proximalend 203 of the rotor shaft 202 is securely mounted to the rotary valve234 through a load coupling interface 239. The load coupling interface239 is formed with the interior ribs 256 which hold a coupling flange241 therein. The coupling flange 241 includes a sidewall 243 thatextends along desired segments of the rotor shaft 202. The sidewall 243includes a base segment 245 and upper segment 247 that extend at leastpartially about the rotor shaft 202. The coupling flange 241 enables therotor shaft 202 to be decoupled (e.g. separately molded) from the rotorvalve 234, thereby offering molding advantages. In addition, thecoupling flange 241 decouples side loads experienced upon the rotorshaft 202 from the rotor valve 234. For example, side loads may beexperienced in various radial directions as noted by arrows 2F which maycause slight deflections of the rotor shaft 202 in the correspondingradial direction. The coupling flange 241 allows a predetermined amountof tilting movement between the rotor shaft 202 and rotor valve 234,such as in the directions of arrows 2F, while the rotor valve 234remains at a relatively fixed orientation with respect to the surface ofthe well plate. As a further example, the rotor valve 234 may bemaintained in a predetermined plane as denoted by coordinate XY.

Returning to FIGS. 2A, 2B, and 3C, the rotary valve assembly 200 ismaintained at a predetermined fixed position on the well plate throughvarious features. The latch arms 226 fixedly locate the valve cap 210 ata predetermined XY position on the well plate 150 relative to the wells156 (FIG. 3C). The detents 158 (FIG. 3C) on the walls of the wells 156hold the latch arms 226 and valve cap 210 downward. The cap extension216 maintains the rotor shaft 202 at a predetermined XY position, andorients and permits rotation around the rotational axis 220. The biasingelement 253 provided about the interior ribs 256 abuts against aninterior shelf 221 provided within an interior cavity 213 within the capbase 214 (FIG. 2B). The interior shelf 221 maintains a downward force onthe biasing element 253, thereby holding the rotor base 240, theinterface ring 260 and the central interface pad 262 firmly against asurface of the well plate 250, while permitting rotation movement.

Illumination Chamber

FIG. 4A illustrates a bottom view of a portion of the cartridge assembly100 to illustrate the illumination chamber 400 in more detail. Theillumination chamber 400 is to receive an illumination element on theinstrument. For example, the illumination element may represent one ormore LEDs. The illumination element is positioned within theillumination chamber 400 in accordance with predefined XYZ coordinates.As explained hereafter, the LED illumination element is inserted into(e.g., docks within) the illumination chamber 400 at a well-defined XYZposition, where the position of the LED illumination element is definedby position limiting features within the illumination chamber 400.

With joint reference to FIGS. 1A, 5C, and 5D, the illumination chamber400 is formed with a circular peripheral wall 406 on one side andposition limiters 408 (FIG. 5D) on an opposite side. The positionlimiters 408 are provided at select points around the fluidics analysisstation 170. The position limiters 408 engage mating features on aperipheral outer wall of the illumination element to position theillumination element at a known desired position, such as in an XYdirection relative to an optical interface window 410 provided on thewell plate 150. In the present example, the XY direction extends in aplane substantially parallel to a surface of the optical interfacewindow 410. In addition, one or more ribs 412 are provided on the wellplate 150 and positioned about the optical interface window 410. Theillumination element abuts against (docks to) the ribs 412 when insertedin the Z-direction (providing a Z datum point for the illuminationelement). The ribs 412 abut against a front face of the illuminationelement to manage movement of the illumination element in theZ-direction (i.e. toward and away from the optical interface window410). Optionally, additional or fewer limiters 408 and ribs 412 may beutilized in connection with managing a position of the illuminationelement. Optionally, the XYZ directions may be oriented in differentmanners.

As described herein in more detail, channel covers are formed over fluidchannels that communicate with the optical interface window 410. By wayof example, the fluid channels may be formed in the upper surface of thewell plate 150 with an open side, such that the channel covers are laserbonded (or otherwise joined with) over the fluid channels.

FIG. 4B illustrates a model side sectional view through the variousstructures provided at the fluidics analysis station 170 once a flowcell cartridge 900 is inserted and an illumination element is insertedinto the illumination chamber in accordance with an example herein. InFIG. 4B, an illumination element 450 is illustrated in an operativeposition above a well plate 150 while a flow cell cartridge 900 isinserted into the flow cell chamber 108. The structures of the wellplate 150, visible in FIG. 4B, include the window 410, ribs 412, ports180, 182 and channel covers 416 and 418. The structures of the flow cellcartridge 900, visible in FIG. 4B, include the top frame 904, flow cellwindow 928, ports 934, and analysis circuit 958. The analysis circuit958 includes the active area 962 and active area ports 964. Theillumination chamber 400 is oriented to extend along an illuminationaxis 4B that extends through the interface window 410, flow cell window928, the transparent layer 429, and the active area 962 within theanalysis circuit 958.

The illumination element 450 is inserted into the illumination chamber400 until resting against the ribs 412 on the well plate 150. The ribs412 defined the Z datum point (Z reference point) for the illuminationelement 450 at a predetermined (e.g. minimum) distance above the window410. Light radiating from the illumination element 450 passes throughthe window 410, the flow cell window 928 and a transparent layer 929 onthe top surface of the analysis circuit 958. The ports 180, 182 in thewell plate 150 manage inlet and discharge of fluid through channelsbelow the channel covers 416, 418. The ports 180, 182 align with ports934 in the top frame 904 of the flow cell cartridge 900, while the ports934 align with ports 968 into the analysis circuit 958. As one directionof flow, fluid may travel in through the channel corresponding tochannel cover 418 and pass downward through ports 180, 194 and 964. Thefluid travels across the active area 962 until discharged from ports964, 934, and 182 into the channel corresponding to channel cover 416.Optionally, the direction of flow may be reversed.

Optionally, one or more electrodes may be positioned proximate to one ormore of the ports 180, 182, 934, or 964 with the electrodes maintainedat a desired voltage. In addition, the analysis circuit may function asan opposite voltage potential to create a voltage potential through thefluid within the active area.

Well Plate

Next, the well plate 150 and a network of fluid channels through thewell plate 150 is described in more detail in connection with FIGS.5A-5E. The well plate 150 provides a low profile channel construction.By way of example, the well plate 150 may be formed with a base layerhaving a network of open sided fluid channels formed on one or bothsides thereof. The top and/or bottom sides of the base layer are joined,in a sealed manner, to a corresponding backing layer (e.g., a plasticfilm) to close the open sides of the fluid channels. For example, whenonly the bottom side of the base layer includes open sided channels, abacking layer may only be provided over the bottom side. Similarly, whenthe top side of the base layer is the only sided includes open sidedchannels, a backing layer may be only provided over the top side. Whenthe top and bottom sides of the base layer include open sided channels,top and bottom backing layers may be provided over the corresponding topand bottom sides of the base layer.

Optionally, one or both of the base and backing layers may be formed asa polypropylene film, thermoplastic elastomer, vulcanized thermoplasticelastomer and the like. The base and backing layers may be joined withone another in various manners, such as laser bonding. The base layerincludes a network of ports extending through the base layer to providea manner to interconnect channels provided on the top or bottom sides ofthe base layer.

All or portions of the base may be formed from a carbon filled blackplastic or similar material. The carbon filling facilitates laserbonding with mating structures and renders the corresponding areas atleast partially nontransparent. By utilizing a black plastic or anothernontransparent material, the well plate 150 affords a desired amount ofimmunity to light exposure and reduces auto fluorescence of a flow cellcartridge by preventing undesired transmission or reflection offlorescent light. The well plate 150 also reduces optical noise withinthe system by preventing undesired transmission or reflection of light.

FIG. 5A illustrates a front perspective view of the well plate 150formed in accordance with an example herein. FIG. 5B illustrates abottom surface of the base 152 of the well plate 150 to betterillustrate an example of a network of open sided channels therein. Asnoted above, a backing layer may be provided over the bottom surface ofthe base 152 to close the open sided channels. The well plate 150includes a valve station 164, pump station 168 and fluidics analysisstation 170. A sample inlet channel 172D extends from the sample inlet124 to a sample transition port 162D. A front surface of the base 152includes the plurality of wells 154, 156 located about the valve station164. A portion of the wells 156 are arranged in a circular pattern abouta valve station 164. Within the valve station 164, a circular flange 166is formed on (and extends upward from) the base 152. The flange 166 hasan internal circular shape that matches the shape of the rotor base 240.The flange 166 and area of the well plate within the flange 166 act as astarter for the rotary valve assembly 200. An internal surface of theflange 166 has an interior diameter that substantially corresponds to anouter diameter of the rotor base 240, thereby forming a guide withinwhich the rotor base 240 rotates. Optionally, the flange 166 may alsofacilitate maintaining the sealed relation between the rotor-base 240and well plate 150.

An array of well transition ports 162 are provided in the base 152within the region interior to the flange 166. The well transition ports162 are formed in a predetermined pattern corresponding to a pattern andrange of motion of the rotary valve assembly 200, such as along acircular arc having a predefined radius. For example, the welltransition ports 162 may be formed along a circle having a radius thatis equal to the length of the fluid channel 246 (FIG. 2C). A centralfeed port 160 is provided at a center of the flange 166 and a center ofthe circle defined by the well transition ports 162. The central feedport 161 is positioned to align with the rotational axis 220 of therotor shaft 202, which also corresponds to the central port 248 formedthrough the rotor valve 234.

The pump station 168 includes first and second support posts 502, 504that extend upward from the base 152. The support posts 502, 504 receivea drive shaft and a syringe arm of the pump assembly 500. The supportposts 502, 504 guide movement of the drive shaft and syringe arm alongpredetermined reciprocating linear paths move fluids through thecartridge assembly 100. The fluidics analysis station 170 delivers fluidto, and removes fluid from, a flow cell.

FIG. 5B illustrates a network of open sided flow channels 172 providedon the bottom surface of the base 152 of the well plate 150. The flowchannels 172 extend through the pump station 168, valve station 164, andfluidics analysis station 170. Additionally or alternatively, the flowchannels 172 may pass through additional stations. The flow channels 172may be formed in various patterns and have varying lengths anddiameters.

FIG. 5E illustrates an enlarged portion of the bottom surface 153 of thebase 152 proximate to the valve station 164. The valve station 164includes the well transition ports 162 arranged in the predeterminedpattern (e.g. circular pattern) corresponding to a path followed by therotary valve assembly 200. The well plate 150 further includes welldischarge ports 163 that extend through the base 152 and open onto a topside of the base 152 within a corresponding well (not visible in FIG.5A). Each well discharge port 163 is joined to a corresponding welltransition ports 162 through a well discharge channel 165. The wellplate 150 includes a plurality of the well discharge channels 165dependent upon the number and position of the wells 154, 156. The welldischarge channels may be shaped in various manners, such as a straightline, serpentine path, U-shaped path and otherwise. In the example ofFIG. 5E, a collection of short straight well discharge channels 165Aextend between corresponding well transition ports 162A and welldischarge ports 163A that align with the smaller closer wells 156 (FIG.5A). A collection of longer straight well discharge channels 165B extendbetween corresponding well transition ports 162B and well dischargeports 163B that align with the larger wells 154 located radially outwardbeyond the wells 156. In addition, cache storage areas 167 are providedthat include storage channels 165C that are loaded and unloaded atstorage ports 162C. At various points during operation, it may bedesirable to temporarily store a portion of the fluid without dumping towaste. Accordingly, the fluid is moved to an available storage channel165C. Optionally, an opposite end of the storage channels 165C mayinclude a port 163C to allow air (or an inert fluid) to enter and leavethe storage channel 165C. Optionally, the ports 163C may be joined tocorresponding storage wells on the well plate 150.

FIG. 5C illustrates a bottom plan view of a portion of the base 152 toprovide a more detailed view of the fluidics analysis station 170 on theback surface of the well plate 150. A flow cell is inserted to alignwith station 170 during operation. The fluidics analysis station 170includes the optical interface window 410, which is bordered diagonallyon opposite corners by interface ports 180 and 182. The interface ports180 and 182 are coupled to ports on a flow cell when the flow cell isinserted. Limit posts 190 and 192 are located along one or more sides ofthe fluidics analysis station 170. The limit posts 190, 192 are engagedby the flow cell when inserted to properly align the flow cell relativeto the optical interface window 410 and interface ports 180, 182 in theXY direction.

The back surface of the well plate 150 also includes ribs 472 thatextend outward (downward) from the bottom surface of the well plate 150.For example, the ribs 472 may align with an extension in the oppositedirection from ribs 412 (FIG. 5D). The bottom surface of the well plate150 also includes a Z position pad 473. An outermost surface of the Zposition pad 473 and the ribs 472 are aligned in a common predeterminedplane to define a Z datum point, at which the flow cell cartridge 900 isto be positioned when loaded. As explained herein, the flow cellcartridge 900 includes a top frame having an upper surface that abutsagainst the Z position pad 473 and ribs 472 to maintain the flow cellwindow and ports at a predetermined Z position relative to the bottomsurface of the well plate at the fluidics analysis station 170.

FIG. 5D illustrates a top plan view of a front/top portion of the base152 corresponding to FIG. 5C to provide a more detailed view of thefluidics analysis station 172 on a front surface of the well plate 150.The front/top portion of the base 152 within the fluidics analysisstation 172 corresponds to the illumination chamber 400 (FIG. 4 ) andaccordingly the reference numbers used in connection with FIG. 4 areutilized in connection with FIG. 5D. As shown in FIG. 5D, positionlimiters 408 are provided along one or more sides of the illuminationstation 172 and engage mating features on a peripheral outer wall of anillumination element. By way of example only, a dashed circular line 414is provided to indicate the footprint of the illumination element onceinserted by the instrument. The position limiters 408 locate theillumination element at a predefined XY coordinate position (where theXY coordinate system extends in a plane substantially parallel to thesurface of the well plate 150 and optical interface window 410).

The well plate 150 includes, on the top side thereof, one or moreinsertion limit elements 411 to register the illumination element of theinstrument at a predetermined distance from the optical interface window410. The insertion limit elements 411 engage an illumination element onthe instrument during a micro-fluidics analysis operation. By way ofexample, the insertion limit elements 411 may include one or more ribs412 that are provided along one or more sides of the optical interfacewindow 410 and project upward from the optical interface window 410 by apredetermined distance that is defined to maintain a desired offsetbetween a distal surface of the illumination element (e.g., a lens) andthe optical interface window 410. The ribs 412 on the top side of thewell plate 150 align with the ribs 472 on the bottom side of the wellplate 150. The ribs 412 locate the illumination element at a predefinedZ-tolerance or Z-coordinate position (where the Z axis of the referencecoordinate system extends in a plane substantially perpendicular to thesurface of the well plate 150 and the surface of the optical interfacewindow 410). By way of example, the ribs 412 may register an LED lightwithin an illumination element to a predetermined surface (e.g. theoptical interface window 410) while minimizing a Z-tolerance between theLED light source on the instrument and the flow cell below the opticalinterface window 410.

Within the valve station 164, a select well transition port 162 iscoupled (through the rotor valve 234) to the central feed port 160. Thecentral feed port 160 is coupled through a channel 174 to a transitionport 176 which transfers the direction of flow to the opposite side ofthe base 152. With reference to FIG. 5A, the transition port 176 isillustrated in the fluidics analysis station 170. An illuminationchannel 178 continues from the transition port 176 to interface port 180which is located proximate to the optical interface window 410. Thefluids pass through flow cell channels on the flow cell until the fluidsare discharged from the flow cell at a flow cell port 182. The fluid isthen conveyed from the interface port 182 along a flow cell channel 184.

FIG. 5D also illustrates in more detail the illumination channels 178and 184 formed in accordance with one example, with the illuminationchannels 178, 184 terminating proximate to the optical interface window410 at corresponding interface ports 180, 182. The illumination channels178, 184 may be formed as open sided channels on the front surface ofthe well plate 150 where the open sides are covered with channel covers416, 418 (FIG. 4 ). The illumination channel 178 begins and terminatesat transition port 176 and interface port 180, respectively. Theillumination channel 184 begins and ends at interface port 182 and apump station port (not visible in FIG. 5D), respectively.

The examples described herein generally described one direction of fluidflow. However, it is recognized that the fluidics analysis operationsmay be performed in connection with fluid flow traveling in the oppositedirection. Additionally or alternatively, fluids may be managed to flowin different directions within the various channels at different stagesof a fluidics analysis. Therefore, to the extent any port, channel orother structure is assigned a name descriptive of a flow direction, itis recognized that such descriptor is merely an example and that theport, channel or other structure may be utilized to convey fluids in theopposite direction.

Syringe Pump Assembly

Next, the syringe pump assembly 500 will be described in connection withan example herein with reference to FIGS. 6A-6E. As explained herein,the syringe pump assembly 500 provides a bidirectional pumping actionthat avoids adverse backlash effects. The syringe pump assembly 500 isreciprocally moved by applying a drive force in one direction andpermitting a biasing force to move a plunger arm in an oppositedirection, thereby avoiding a need to apply a pulling force to the pumpassembly 500.

FIG. 6A illustrates a top plan view of the pump station 168 on the wellplate 150 provided in accordance with an example herein. The pumpstation 168 includes a pump channel segment 506 that is joined at oneend to a station inlet port 508 and at an opposite end to a stationdischarge port 510. The pump channel segment 506 may be functionallydivided into a preparation segment 512, a discharge segment 514 and apump work segment 516, all of which are formed continuous with oneanother to support fluid flow in either direction. The work segment 516includes a work area 513, in which a plunger 540 moves in areciprocating manner to introduce alternately a low pressure (e.g.vacuum) and high pressure. The work area 513 is sandwiched between apair of pinch valves 518 located upstream and downstream of the workarea 513. The pinch valves 518 determine the direction of flow from thework area 513, such as toward waste or towards a flow cell. By way ofexample, the pinch valves 518 may be formed by pressing a material ofinterest (e.g. a thermoplastic elastomer) into a circular indentationsformed along the channel within the work segment 516. As explainedherein, the pinch valves 518 are alternately opened and closed in acoordinated manner in connection with the introduction of low pressureand high pressure states within the work area 513 to pull or push fluidthrough the pump station 168. The preparation segment 512 is locatedupstream of the work segment 516 between the work segment 516 and thestation inlet port 508. The present example, the preparation segment 512includes a channel that is arranged in a serpentine shape to form astorage area within the pump channel segment 506 to hold a predeterminedamount of fluid before the fluid passes through the work segment 516.Optionally, the preparation segment 512 may be lengthened or shortenedor entirely eliminated, such as by providing the station inlet port 508proximate an end of the work segment 516. The discharge segment 514 islocated downstream of the work segment 516 between the work segment 516and the station discharge port 510. In the present example, thedischarge segment 514 is provided as a relatively short straightchannel, all thorough alternative configurations may be provided withthe discharge segment 514 varying in length and pattern, or removedentirely.

FIG. 6B illustrates a side view of a plunger 540 provided within thepump 500. The plunger 540 generally includes a drive arm 546 and aplunger arm 554 that are joined with one another through a bridgesegment 552, all of which are formed together in a monolithic structure(e.g., molded together). The drive arm 546 has a drive end 548 and adistal end 549. The plunger arm 554 includes a work end 556 and a distalend 558. A plunger element 557 that is mounted on the work end 556 ofthe plunger arm 554. The distal ends 549 and 558 of the drive arm 546and plunger arm 554 are joined to the bridge segment 552. The plungerarm 554 and drive arm 546 extend downward from the bridge segment 552 ina common direction with the plunger arm 554. The plunger arm 554 isoriented to extend in a direction substantially parallel to the lengthof the drive arm 546 such that the drive arm 546 and plunger arm 554move together in a common direction and alignment in response to a driveforce 543 and a bias force 544. The drive force 543 and bias force 544represent uni-directional pushing forces without a corresponding reversepulling force. The bridge segment 552 includes a biasing surface 542that is positioned at, and exposed through, the pump access opening 123(FIG. 1A) formed in the cover 102. A biasing element of the instrument(e.g. a spring) is to engage, and apply a biasing force against, thebiasing surface 542. The drive end 548 of the drive arm 546 ispositioned at a drive opening 116 in the bottom surface 110 of thecartridge assembly 100 (FIG. 1B) to be engaged by the pump driveassembly of the instrument. The pump drive assembly intermittentlyapplies and removes a drive force 543 to and from the drive arm 546. Thedrive end 548 and biasing surface 542 are located at opposite ends ofthe plunger 540. The drive end 548 and biasing surface 542 are exposedat upper and lower surfaces of the housing of the cartridge assembly 100such that corresponding unidirectional drive and biasing forces 543, 544are applied thereto in connection with moving the plunger 540 in areciprocating motion without introducing backlash, while providingdirect instrument encoder measurements. The drive and biasing forces543, 544 apply a bi-directional push system which avoids the need for apush/pull pump driver.

FIG. 6C illustrates an enlarged side view of the plunger element 557 asmounted to the plunder arm 554. The plunger element 557 is illustratedin a partially transparent manner to illustrate internal structures. Theplunger arm 554 includes a leading edge 553, to which one or more stems559 are formed integrally and in a monolithic structure there with. Thestems 559 include a hinge pin 565 extending there between. A supportbeam 551 is provided with an eye 545 in a proximal end thereof. The eye545 is elongated and receives hinge pin 565 such that the support beam551 is movable over a slight predetermined range in the direction ofarrow 567 which extends generally parallel to a length of the plungerarm 554 and plunger element 557. Optionally, the stem and support beam559, 551 may be formed as a common monolithic structure.

The plunger element 557 includes a body 561 that is formed in agenerally tubular shape with predetermined contours about a periphery ofthe body 561. The body 561 includes a trailing edge 555 that is formedin a row with the leading edge 553 of the plunger arm 554 (e.g. througha cold molding operation). The body 561 includes one or more peripheralplunger ribs 563 extending there about that are shaped and positioned tomaintain an airtight seal within the interior passage of the supportpost 504, in which the plunger arm 554 reciprocates.

The plunger element 557 may be formed from a vulcanized thermoplasticelastomer (TPV) or other material that is relatively more flexible andcompressible than the plunger arm 554. The drive arm 546, bridge segment552, and plunger arm 554 are formed from a relatively hard plasticmaterial (e.g., polycarbonate plastic). The plunger element 557 isformed to the plunger arm 554 in a non-snap on manner. As one example,the plunger arm 554 may be molded over the stem 559 and support beam551. By way of example, a two shot molding process may be used, whereinthe plunger arm 554 is molded during an initial molding operation, whilethe plunger element 557 is added during the second molding operation. Byutilizing a molding process, the plunger element 557 is secured to theplunger arm 554 with relatively little or no tolerance or clearancethere between (at the leading and trailing edges 553, 555), with theplunger element 557 and plunger arm 554 physically and chemicallyinterlocked to one another (at the leading and trailing edges 553, 555).

By providing a close tolerance between the plunger element 557 and theplunger arm 554, the plunger 540 substantially eliminates or avoids“hysteresis” that might otherwise occur if the plunger element 557 weremerely snapped on or otherwise more loosely attached to the plunger arm554. In addition, by molding the plunger element 557 over the supportbeam 551 and stem 559, a final structure is provided that facilitatesavoidance of hysteresis.

The non-snap on interface between the plunger element 557 and plungerarm 554 affords improvements over a snap on type plunger element whichwould introduce the potential for the plunger element to move upward anddownward relative to the plunger arm each time the direction of motionis changed. When movement is experienced between a snap on plunger andplunger arm, such a configuration creates a potential for backlash, alsoreferred to as hysteresis.

In accordance with examples herein, the plunger 540 moves in bothdirections numerous times (e.g. a few hundred or thousand pump cyclesper run) during operation. The plunger 540 may move at a speed between0.3 mm/sec to 10 mm/sec. Thus, a snap on type plunger element wouldcreate the potential for backlash or hysteresis numerous timesthroughout a run (e.g. a micro-fluidics analysis operation). By formingthe plunger element 557 on a portion of the plunger arm 554 (in anon-snap on manner), examples herein avoid the risk of hysteresis orbacklash by maintaining a fixed relation there between.

Returning to FIG. 6B, during operation, the pump drive assembly of theinstrument intermittently applies a drive force 543 to the drive end 548of the drive arm 546 to move the plunger 540 upward in the direction ofthe drive force 543. When the drive force 543 is removed, the biasingforce 544 moves the plunger 540 downward in the direction of the biasingforce 544. By applying a biasing force 544, examples herein avoid theneed for the pump drive assembly to attach to the drive arm 546 and toavoid the need to apply a pulling force to the drive arm 546. The driveforce 543 is intermittently applied and removed, thereby causing theplunger 542 move upward and downward repeatedly throughout operation. Asthe plunger 540 moves upward and downward, the work and 556 introduceslow pressure and high pressure states within the work area 513 (FIG.6A). As the high and low pressure states are introduced into the workarea 513, fluid is pulled and pushed along the channel segment 506. Thedirection of movement of the fluid through the pump channel segment 506is controlled by opening and closing the pinch valves 518.

FIG. 6D illustrates a side sectional view of the pump station 168 tobetter illustrate the pumping operation. Within the pump station 168, apushpin brace 560 is mounted to a lower surface of the base 152 of thewell plate 150. The brace 560 includes support posts 562 that havepassages 564 therein. The passages 564 receive corresponding pushpins520, 521. The pushpins 520, 521 include shafts 523 that include workends 566 and opposite contact pads 524. The work ends 566 are positionedat the pinch valves 518, while the contact pads 524 are flared radiallyoutward beyond outer ends of the support posts 562. The shafts 523include one or more exterior ribs 525 extending thereabout. The passages564 also include one or more interior ribs 527. The exterior andinterior ribs 525, 527 cooperate to retain the pushpins 520, 521 withinthe corresponding passages 564, while permitting the pushpins 520, 521to move back and forth along the support posts 562 in a valve openingdirection 519 and a valve opening direction 517. The contact pads 524are positioned at the pushpin openings 114 (FIG. 1B) in the bottomsurface 110.

During operation, a valve drive element of the instrument is positionedto engage the contact pads 524. The valve drive element applies a valveclosing force (in the valve closing direction 519) to one of thepushpins 520, 521, while applying no closing force to the other pushpin520, 521. When no valve closing force is applied to a pushpin 520, 521,the pushpin 520, 521 moves in the valve opening direction 517 to a valveopen state, such that the corresponding pinch valve 518 is open. When avalve closing force is applied and the corresponding pushpin 520, 521moves in the valve closing direction 519, the corresponding pinch valve518 is closed. The pushpins 520, 521 and the corresponding pinch valves518 alternately move between open and closed states.

FIG. 6D also illustrates the plunger arm 554 when loaded within thesupport post 504. The plunger arm 554 reciprocally moves in a pullingdirection 566 and a pushing direction 568 to create corresponding lowpressure and high pressure states, respectively, in the work area 513.As the plunger arm 554 is moved in the pulling direction 566, fluid isdrawn into the work area 513, where the amount of fluid drawn into thework area 513 is dependent upon the range of motion of the plunger arm554. When the syringe arm is moved in the pushing direction 568, thefluid within the work area 513 is pushed from the work area 513 backinto the flow channel. The direction in which fluid is drawn into thework area 513 from the fluid channel depends on which of the pushpins520, 521 have closed the corresponding pinch valve 518. For example, tointroduce a pulling force in the direction of arrow A, the pushpin 521would be moved to the closed state to close the corresponding pinchvalve 518 while the syringe arm is moved in the pulling direction 566.As the plunger arm 554 withdraws from the work area 513, fluid advancesalong the flow channel in the direction of arrow A. When the plunger arm554 reaches an end of a range of motion, the pushpin 521 is released andpermitted to move in the opening direction 517 to permit thecorresponding pinch valve 518 to open. At the same time, the pushpin 520is moved in the closing direction 519 to close the corresponding pinchvalve. Thereafter, the plunger arm 554 is moved in the push direction568 to force the fluid from the work area 513 into the fluid channel inthe direction of arrow B. When it is desirable to move fluid in theopposite direction, the operation of the pushpins 520, 521 is reversedrelative to movement of the plunger arm 554.

FIG. 6E illustrates an enlarged side perspective view of a portion ofthe plunger 540 inserted into the support post 502, 504. The plunger arm554 is slidably received within the support post 504, while the drivearm 546 is slidably received within the support shaft 502. The supportshaft 502 and drive arm 546 are formed with a cross section that is Xshaped in order to guide the plunger 540 along a predeterminedreciprocating path with a relatively small tolerance for error.

FIG. 6F illustrates a perspective view of the support shaft 504 toreceive the plunger arm 554 in accordance with examples herein. Thesupport shaft 504 includes a proximal end 570 and a distal end 571. Theproximal end 570 is mounted on the well plate 150 at the pump station168, while the distal end 571 extends upward from the pump station 168.The support shaft 504 is elongated and includes a passage 572 extendingbetween the proximal and distal ends 570, 571. The passage 572 has afirst interior diameter 571 for a segment of the passage 572 thatextends from the distal end 571 toward an area near the proximal end570. The passage 572 has a second larger diameter 576 at the proximalend 570 to form a parking station 574. The parking station 574 is toreceive at least the portion of the plunger element 557 that includesthe plunger ribs when located in a storage position. The plunger element557 may be located at the parking station 574 during storage,transportation, or generally when not in use. By allowing the plungerribs of the plunger element 557 to be retained in the parking station574 with an enlarged diameter, examples herein avoid creep of theplunger element 557 such that the plunger element 557 and plunger ribsmaintain an original shape for a longer period of time without beingunduly compressed. Otherwise, creep (or changes in the shape) of theplunger element 557 and plunger ribs may result if stored for extendedperiods of time within the portion of the passage 572 having the firstnarrower diameter 575.

Fluidics Instrument

FIG. 7 illustrates a block diagram of a fluidics instrument 700implemented in accordance with an example herein. The instrument 700includes a docking station 703 to receive a cartridge assembly 100.Various electrical, optical and mechanical subassemblies within theinstrument 700 interact with the cartridge assembly 100 during amicro-fluidics analysis operation.

The instrument 700 includes, among other things, one or more processors702 that are to execute program instructions stored in memory 704 inorder to perform the micro-fluidics analysis operations. The processor702 is communicatively coupled to a valve drive assembly 710, pump driveassembly 720, a piercer actuator assembly 740, an illumination element750, an electrical contact array 752, and a heating element 753.

A user (U/I) interface 706 is provided for users to control and monitoroperation of the instrument 700. One or more communications interfaces708 convey data and other information between the instrument 700 andremote computers, networks and the like. For example, the communicationsinterface 708 may receive protocols, patient records, and otherinformation related to a particular fluidics analysis operation. Thecommunications interface 708 may also convey raw resultant data, as wellas data derived from analysis of one or more samples.

The valve drive assembly 710 includes a drive shaft 712 to engage therotary valve assembly 200. The valve drive assembly 710 also includes arotation motor 714 and a translation motor 716. The translation motor716 moves the drive shaft 712 in a translational direction 718 betweenan engaged state and a disengaged state with the rotor shaft 202 of therotor valve assembly 200. Once the drive shaft 712 is physically andsecurely engaged with the rotor valve assembly 200, the rotation motor714 manages rotation of the drive shaft 712 in a rotary direction 719 todirect the rotary valve assembly 200 to connect and disconnect variouswells of reagents to the channels of the well plate.

The valve drive assembly 710 includes a position encoder 713 thatmonitors a position of the drive shaft 712 relative to the rotor shaft202 (FIG. 2B). The encoder 713 provides position data to the processor702 in order to ensure that the splines of the drive shaft 712 are fullyengaged with the interior splines 232 of the rotor shaft 202, therebyensuring that the position encoder 713 closely tracks the rotationalposition of the rotor shaft 202. By way of example, the encoder 713 mayinclude a shaft having a male encoder spline configuration that isshaped and dimensioned to match the interior splines 232 (FIG. 2B)described above in connection with the rotary valve assembly 200. Theencoder splines fully made with and bottom out within the interiorsplines 232 to maintain a fixed relation there between. The encodersplines do not apply a driving force, but instead merely follow movementof the rotor shaft 202 to provide precise and accurate angular positiondata to the processor 702. The drive shaft 712 includes a separate setof drive splines that fit over the distal end of the rotor shaft 202.The drive splines fit between and apply a driving force to the exteriorsplines 230 on the rotor shaft 202.

By maintaining the rotor and drive shafts 202, 712 in a fixed rotationalrelation, the processor 702 can utilize rotational data obtained fromthe motor 714 to determine the particular rotational position of therotary valve 234.

The valve drive assembly 710 is to move (e.g., rotate) the rotor shaft202 in order to selectively connect the flow channels to one or more ofthe ports. In many operations, the rotor shaft 202 is rotated varyingdegrees based on locations of well ports for reagent wells that aresuccessively utilized. For example, when adjacent wells are utilized inorder, the valve drive assembly 710 will rotate the rotor shaft 202 onlya few degrees. However, when first and second wells are to be used thatare on opposite sides of the well plate, the valve drive assembly 710will rotate the rotor shaft 202 180. degree. or more or less. Afterrotating the rotor shaft 202, the rotor valve assembly 200 ismomentarily stationary to permit a fluid to flow therethrough or topermit a sample to be detected.

The piercer actuator assembly 740 includes one or more piercer shafts742 and a translation motor 744 to drive the piercer shafts 742 betweenretracted and extended positions. When the piercer shafts 742 are movedto the extended position, the piercer shaft 742 engages an upper surfaceof the piercing unit 300 and forces the piercing unit 300 downward tocause the piercing elements on the piercing unit 300 to puncture foilscovering corresponding reagent wells. The piercing shafts 742 may remainextended throughout a fluidics analysis operation, or alternatively maybe retracted.

A pump drive assembly 720 includes a pump shaft 722 that is coupled to amotor 724 and moves between extended and retracted positions along apump direction 723. By way of example, the pump shaft 722 may be formedas a screw shaft that is rotated in the directions of arrow 721. Bychanging the direction in which the pump shaft 722 is screwed, the pumpshaft 722 moves inward (in a retracted direction) and outward (in anextended direction) along the pumping direction 723. By repeatedlymoving the shaft 723 between retracted and extended positions, the pumpshaft 722 applies drive forces 543 to the drive arm 546 to move the pumpassembly 500 in a direction that causes the syringe arm 554 to create alow-pressure state at the work area to draw/pull fluid into the pumpingstation. The drive shaft 722 is repeatedly moved to the retractedposition, and a biasing element 734 applies a biasing force to thebiasing surface 542 on the pump assembly 500 to move the pump assembly500 downward in the direction of the biasing force 544, thereby causingthe syringe arm 554 to form a high-pressure state at the work area topush fluid from the pumping station.

A position encoder 735 is provided with the biasing element 734. Theposition encoder 735 tracks a position of the biasing element 734 as thebiasing element 734 moves upward and downward with the plunger 540. Theposition encoder 735 provides position data to the processor 702 inorder to track the position of the plunger 540 throughout operation.

The pump drive assembly 720 also includes valve drive shafts 726 and 728that are positioned to align with the pushpins 520, 521. The valve driveshafts 726, 728 move between extended and retracted positions alongarrow 725 by a motor 730. The valve drive shafts 726, 728 are moved inopposite directions, such that when the valve drive shaft 726 isextended, the valve drive shaft 728 is retracted, and vice versa. Thevalve drive shafts 726, 728 are moved in opposite directions in analternating manner, synchronized with movement of the pump shaft 722, inorder to move fluid through the pump station 168, and thus through theflow cell.

The illumination element 756 is moved into and out of the illuminationchamber 400. The illumination element 750 includes an optics system toprovide one or more types of illumination light into the eliminationchamber 400. By way of example, the elimination element 756 may includean LED light tube and the like, to generate a desired amount and type oflight. An electrical contact array 752 and a heating element 753 areinserted into a flow cell cartridge access area 112 in the bottomsurface 110 of the cartridge assembly 100. The contact array 752 engagesa corresponding array of electrical contact pads 950 on the flow cellcartridge 900. The heating element 753 engages a heat spreader withinthe flow cell cartridge 900.

In accordance with at least one example, the processor 702 managesoperation of the motors, optics, contact arrays and the like.Optionally, numerous processors may be provided that cooperate (e.g.under control of the processor 702) to manage operation of each of themotors, optics, contact arrays, assemblies and components described inconnection with the instrument 700.

By way of example, the motors may be direct drive motors. However, avariety of alternative mechanisms may be used, such as direct current(DC) motors, solenoid drivers, linear actuators, piezoelectric motors,and the like.

Fluidics Control System

FIG. 8 is a schematic view of a computer system 800, implemented by theinstrument 700 of FIG. 7 , in accordance with one example. For example,the computer system 800 may be implemented by one or more processors 702under control of the user interface 708 and program instructions storedin memory 704. Although FIG. 8 shows representative illustrations orblocks of the various components of the computer system 800, it isunderstood that FIG. 8 is merely schematic or representative and thatthe computer system 800 may take various forms and configurations.

The computing system 800 may communicate with the various components,assemblies, and systems (or sub-systems) of the instrument. Thecomputing system 800 may include a fluid-selector module 851, afluidic-control module 852, a detector module 853, a protocol module854, an analysis module 855, a pump drive module 857, a valve drivemodule 859 and an illumination management module 861. Although themodules 851-861 are represented by separate blocks, it is understoodthat each of the modules may be hardware, software, or a combination ofboth and that each of the modules may be part of the same component,such as a processor. Alternatively, at least one the modules 851-861 maybe part of a separate processor. Moreover, each of the modules 851-861may communicate with each other or coordinate commands/instructions forperforming a particular function.

The computing system 800 and/or the modules 851-861 may include anyprocessor-based or microprocessor-based system, including systems usingmicrocontrollers, reduced instruction set computers (RISC), applicationspecific integrated circuits (ASICs), field programmable gate array(FPGAs), logic circuits, and any logic-based device that is capable ofexecuting functions described herein. The above examples are exemplaryonly, and are thus not necessarily intended to limit the definitionand/or meaning of the terms modules or computing system. In theexemplary example, the computing system 800 and/or the modules 851-861execute a set of instructions that are stored in one or more storageelements, memories, or modules in order to generate a sample, obtaindetection data, and/or analyze the detection data.

The set of instructions may include various commands that instruct theinstrument 802 to perform specific operations such as the methods andprocesses of the various examples described herein. The set ofinstructions may be in the form of a software program. As used herein,the terms “software” and “firmware” are interchangeable, and include anycomputer program stored in memory for execution by a computer, includingRAM memory, ROM memory, EPROM memory, EEPROM memory, and non-volatileRAM (NVRAM) memory. The above memory types are exemplary only, and arethus not limiting as to the types of memory usable for storage of acomputer program.

The software may be in various forms such as system software orapplication software. Further, the software may be in the form of acollection of separate programs, or a program module within a largerprogram or a portion of a program module. The software also may includemodular programming in the form of object-oriented programming.

The computing system 800 is illustrated conceptually as a collection ofmodules, but may be implemented utilizing any combination of dedicatedhardware boards, DSPs, processors, etc. Alternatively, the computingsystem 800 may be implemented utilizing an off-the-shelf PC with asingle processor or multiple processors, with the functional operationsdistributed between the processors. As a further option, the modulesdescribed herein may be implemented utilizing a hybrid configuration inwhich certain modular functions are performed utilizing dedicatedhardware, while the remaining modular functions are performed utilizingan off-the-shelf PC and the like. The modules also may be implemented assoftware modules within a processing unit. One or more of thecomputational modules can be located, for example, in a network or in acloud computing environment.

As explained herein, the valve drive assembly and pump drive assemblyinclude encoders that transmits signals to the computing system 800 thatare indicative of rotational and translational positions of thecorresponding components (e.g., the rotor valve and plunger).

In some examples, the detector module 853 may command an imagingassembly (that includes the illumination element 750 and the analysiscircuit within the flow cell cartridge) to image a portion of an imagingwindow (which includes the interface window 410, flow cell window 928and transparent layer of the analysis circuit 958), which may includecommanding an excitation source (the illumination element) to direct anincident light onto the imaging window to excite labels in the samplewithin the active area of the analysis circuit 958. The detector module853 communicates through the contact array 752 and contact pads 950 withthe analysis circuit 958 to obtain image data. In the case of SBSsequencing, each image includes numerous point sources of light from DNAclusters. Also shown, the fluid-selector module 851 may command thevalve drive assembly to move the rotary valve assembly. Thefluidic-control module 852 may command the various pumps and valves tocontrol a flow of fluids. The protocol module 854 may includeinstructions for coordinating the operations of the system 800 so that adesignated protocol may be executed. The protocol module 854 may alsocommand any thermal control elements to control a temperature of thefluid. By way of example only, protocol module 854 may be asequencing-by-synthesis (SBS) module to issue various commands forperforming sequencing-by-synthesis processes. In some examples, theprotocol module 854 may also process detection data. After generatingthe amplicons through bridge PCR, the protocol module 854 may provideinstructions to linearize or denature the amplicons to make sstDNA andto add a sequencing primer such that the sequencing primer may behybridized to a universal sequence that flanks a region of interest.Each sequencing cycle extends the sstDNA by a single base and isaccomplished by modified DNA polymerase and a mixture of four types ofnucleotides delivery of which can be instructed by the protocol module854. The different types of nucleotides have unique fluorescent labels,and each nucleotide has a reversible terminator that allows only asingle-base incorporation to occur in each cycle. After a single base isadded to the sstDNA, the protocol module 854 may instruct a wash step toremove non-incorporated nucleotides by flowing a wash solution throughthe flowcell. The protocol module 854 may further instruct theillumination element and the analysis circuit to perform an imagesession(s) to detect the fluorescence in each of the four channels(i.e., one for each fluorescent label). After imaging, the protocolmodule 854 may instruct delivery of a deblocking reagent to chemicallycleave the fluorescent label and the terminator from the sstDNA. Theprotocol module 854 may instruct a wash step to remove the deblockingreagent and products of the deblocking reaction. Another similarsequencing cycle may follow.

Exemplary protocol steps that can be coordinated by protocol module 854include fluidic and detection steps used in reversible terminator-basedSBS methods, for example, as set forth herein or described in US PatentApplication Publication No. 2007/0166705 A1, US Patent ApplicationPublication No. 2006/0188901 A1, U.S. Pat. No. 7,057,026, US PatentApplication Publication No. 2006/0240439 A1, US Patent ApplicationPublication No. 2006/0281109 A1, PCT Publication No. WO 05/065814, USPatent Application Publication No. 2005/0100900 A1, PCT Publication No.WO 06/064199 and PCT Publication No. WO 07/010251, each of which isincorporated herein by reference in its entirety. Exemplary reagents forreversible terminator-based SBS are described in U.S. Pat. Nos.7,541,444; 7,057,026; 7,414,116; 7,427,673; 7,566,537; 7,592,435 and WO07/135368, each of which is incorporated herein by reference in itsentirety. Protocol steps and reagents used in commercial sequencingplatforms such as the GA, HiSeq® and MiSeq® platforms from Illumina,Inc. (San Diego, Calif.) can also be used.

In some examples, the protocol module 854 may issue various commands forperforming the steps of a pyrosequencing protocol. Exemplary stepsinclude those set forth below and in the references cited below.Pyrosequencing detects the release of inorganic pyrophosphate (PPi) asparticular nucleotides are incorporated into the nascent strand(Ronaghi, M. et al. (1996) “Real-time DNA sequencing using detection ofpyrophosphate release.” Analytical Biochemistry 242(1), 84-9; Ronaghi,M. (2001) “Pyrosequencing sheds light on DNA sequencing.” Genome Res.11(1), 3-11; Ronaghi, M. et al. (1998) “A sequencing method based onreal-time pyrophosphate.” Science 281(5375), 363; U.S. Pat. Nos.6,210,891; 6,258,568 and 6,274,320, the disclosures of which areincorporated herein by reference in their entireties). Inpyrosequencing, released PPi can be detected by being immediatelyconverted to adenosine triphosphate (ATP) by ATP sulfurylase, and thelevel of ATP generated is detected via luciferase-produced photons. Inthis case, the reaction valve 816 may include millions of wells whereeach well has a single capture bead having clonally amplified sstDNAthereon. Each well may also include other smaller beads that, forexample, may carry immobilized enzymes (e.g., ATP sulfurylase andluciferase) or facilitate holding the capture bead in the well. Theprotocol module 854 may issue commands to run consecutive cycles offluids that carry a single type of nucleotide (e.g., 1st cycle: A; 2ndcycle: G; 3rd cycle: C; 4th cycle: T; 5th cycle: A; 6th cycle: G; 7thcycle: C; 8th cycle: T; and on). When a nucleotide is incorporated intothe DNA, pyrophosphate is released thereby instigating a chain reactionwhere a burst of light is generated. The burst of light may be detectedby the detector assembly. Detection data may be communicated to theanalysis module 855 for processing.

In some examples, the user may provide user inputs through the userinterface to select an assay protocol to be run by the system. In otherexamples, the system may automatically detect the type of flow cellcartridge that has been inserted into the instrument 802 and confirmwith the user the assay protocol to be run. Alternatively, the systemmay offer a limited number of assay protocols that could be run with thedetermined type of flow cell cartridge. The user may select the desiredassay protocol, and the system may then perform the selected assayprotocol based on preprogrammed instructions.

The analysis module 855 may analyze detection data that is obtained bythe analysis circuit within the flow cell cartridge. Although not shown,the instrument may also include a user interface that interacts with theuser. For example, the user interface may include a display to displayor request information from a user and a user input device to receiveuser inputs. In some examples, the display and the user input device arethe same device (e.g., touch-sensitive display).

In some examples, nucleic acids can be attached to a surface andamplified prior to or during sequencing. Protocol module 854 can includeinstructions for the fluidic steps involved in an amplification process.For example, instructions can be provided for a bridge amplificationtechnique used to form nucleic acid clusters on a surface. Useful bridgeamplification methods are described, for example, in U.S. Pat. No.5,641,658; U.S. Patent Publ. No. 2002/0055100; U.S. Pat. No. 7,115,400;U.S. Patent Publ. No. 2004/0096853; U.S. Patent Publ. No. 2004/0002090;U.S. Patent Publ. No. 2007/0128624; and U.S. Patent Publ. No.2008/0009420. Another useful method for amplifying nucleic acids on asurface is rolling circle amplification (RCA), for example, as describedin Lizardi et al., Nat. Genet. 19:225-232 (1998) and US 2007/0099208 A1,each of which is incorporated herein by reference. Emulsion PCR on beadscan also be used, for example as described in Dressman et al., Proc.Natl. Acad. Sci. USA 100:8817-8822 (2003), WO 05/010145, or U.S. PatentPubl. Nos. 2005/0130173 or 2005/0064460, each of which is incorporatedherein by reference in its entirety.

In some examples, the system is operated with minimal user intervention.For example, the generating and analyzing operations may be conducted inan automated manner by an assay system. In some cases, a user may onlyload the cartridge assembly and activate the instrument to perform theprotocol.

Flow Cell Cartridge

Next, a flow cell cartridge 900 is utilized in accordance with at leastone example herein.

FIG. 9A illustrates a top perspective view of a flow cell cartridge 900formed in accordance with an example herein. The flow cell cartridge 900generally includes top and bottom frames 904 and 906 that are joined toform a generally rectangular structure that is elongated along a loadingdirection 9A. The loading direction 9A corresponds to the direction inwhich the flow cell cartridge 900 is loaded into the flow cell chamber108 of the cartridge assembly 100. The flow cell cartridge 900 includesa loading end 908, a trailing end 910, and lateral side edges 912. Theloading end 908 and side edges 912 include one or more positioningfeatures to mate with corresponding features within the flow cellchamber 108 of the cartridge assembly 100 to ensure proper alignmentwithin the flow cell chamber 108 in the XYZ directions.

Optionally, the top and bottom frames 904 and 906 may be formed from aconductive plastic, such as to provide electrostatic discharge (ESD)protection.

Optionally, the top frame 904 may include a gripping feature 920, suchas a series of ribs extending upward from the top frame 904. Thegripping features 920 facilitate gripping of the flow cell cartridge 900by a user. Optionally, the grooves within the gripping feature 920 maybe shaped to form an indication of direction, such as by shaping theribs to form an arrow, thereby to further provide information to a userregarding a direction in which the flow cell cartridge 900 should beinserted.

FIG. 9B illustrates an enlarged view of a portion of the top frame 904to better illustrate an optical fluidic (0-F) interface to the flow cellcartridge. With joint reference to FIGS. 9A and 9B, the top frame 904includes an O-F interface 940 to communicate with optical and fluidicscomponents of the cartridge assembly 100. The O-F interface 940 includesa flow cell window 928 aligned with an analysis circuit (and describedbelow in more detail in connection with FIGS. 9D and 9E) that is housedwithin the flow cell cartridge 900. The flow cell window 928 permitslight from an illumination element of the instrument to be directed ontothe analysis circuit. The flow cell window 928 may be formed from glassor a similar transparent material, with the glass arranged in asubstantially common plane with an upper surface of the top frame 904.By maintaining the glass within the flow cell window 928 in a planaralignment with the upper surface of the top frame 904, the Z position offlow cell window 928 may be more accurately monitored by monitoring theZ position of the upper surface of the top frame 904.

Flow cell ports 934 are located proximate to the flow cell window 928,where the flow cell ports 934 convey fluid from the cartridge assembly100 through an active area within the analysis circuit. The ports 934are provided within gasket seals 930 that are formed in an elongatedmanner. In the example of FIG. 9A, the gasket seals 930 are oriented toextend generally parallel to one another and arranged at an acute anglerelative to the loading direction 9A. The flow cell ports 934 within thegasket seals 930 are positioned to mate with corresponding ports withinthe flow cell chamber 108 of the cartridge assembly 100.

Seals 930 are provided on opposite sides of the flow cell window 928. Byway of example, the seals 930 may be oriented diagonally across the flowcell window 928 from one another. The seals 930 may be formed from TPEor another similar material. The seals 930 fit in cavities formed in thetop frame 904 that are in fluid communication with injection gates 932.During a manufacturing process, TPE is injected through the injectiongates 932 and permitted to flow through an internal channel within thetop frame until forming as the seals 930. The injection molding processboth physically and chemically bonds the seals 930 to the top frame 904in order to maintain the seals 930 at a predefined position on the topframe 904 (to remain within a select tolerance). The gasket seals 930provide a low profile, miniaturized seal configuration that affords adesired tolerance buildup (e.g. minimizing tolerance buildup).

Returning to FIG. 9A, the top frame 904 includes ribs 922 that areelongated and oriented to extend in a direction common (e.g. parallel)with the loading direction 9A. The ribs 922 provide a loading protectionfeature such that, as the flow cell cartridge 900 is loaded into theflow cell chamber, the gasket seals 930 and flow cell ports 934 do notcontact or otherwise engage housing features surrounding the flow cellchamber 108. In addition, the ribs 922 may provide a standoff feature,such that in the event that the flow cell cartridge 900 is laid upsidedown on a table or other structure, the ribs 922 may prevent otherfeatures on the top frame 904 from touching dust and other material on asurface where the flow cell cartridge 900 is placed.

The top frame 904 includes one or more Z-position features(corresponding to a Z-datum point) that is utilized to register the LEDlight tube within the illumination element of the instrument to the flowcell window 928 of the flow cell cartridge 900. For example, the topsurface of the top frame 904 abuts against the ribs 472 and pad 473 onthe bottom surface of the well plate 150 to define a Z datum point forthe flow cell cartridge 900. The Z-position limit feature affords adesired tolerance (e.g. a minimized tolerance) between the light sourceof the illumination element in the instrument and the flow cellcartridge.

FIG. 9C illustrates a bottom perspective view of the flow cell cartridgeof FIG. 9A. The lower shell 906 is formed with one or more standoffs 914that are located near the loading and trailing ends 908 and 910.Optionally, the standoffs 914 may be located in other positions on thebottom frame 906. Additionally or alternatively, more or fewer standoffs914 may be utilized. The standoffs 914 maintain a predetermined spacingbetween the features within the bottom frame 906 and any surface onwhich the flow cell cartridge 900 is set. For example, when storing thecartridge 900 on a desk, lab bench, storage area or otherwise, thestandoffs 914 prevent the features in the bottom frame 906 fromcontacting dust and other particulate material on the desk, lab benchand the like. In addition, the standoffs 914 may be shaped anddimensioned as alignment keying features to prevent the flow cellcartridge 900 from being inserted incorrectly into the cartridgeassembly 100 (e.g. backwards). For example, the standoffs 914 may beformed with different sizes, such as different lengths, thicknesses,standoff heights and the like. In the example of FIG. 9C, the standoff914 that is proximate to the loading end 908 is shorter in length, ascompared to a length of the standoff 914 that is located proximate tothe trailing end 910.

The bottom frame 906 includes an opening 944 that is aligned with theoptical-fluidics interface 940 on the top frame 904 (and the heatspreader 955 on the PCB 952). The opening 944 exposes a back side of aportion of the analysis circuit. The bottom frame 906 also includescontact pad openings 946 that are aligned with and expose arrays ofcontact pads 950 that are provided with the analysis circuit. Thecontact pad openings 946 are separated by a cross bar 948 that maintainsa width of the contact pad openings 946 sufficiently small to preventinadvertent insertion of undesired objects that might otherwise damagethe contact pads 950 (e.g., a user's finger, test equipment, etc.). Inthe present example, the contact pad openings 946 are rectangular andeach expose two or more rows of contact pads 950.

FIG. 9D illustrates a top view of a portion of a printed circuit board952 provided within the flow cell cartridge 900 formed in accordancewith an example herein. The printed circuit board 952 includes a topsurface 956 that includes an analysis circuit 958. By way of example,the analysis circuit 958 may represent a CMOS circuit. The analysiscircuit 958 is to support flow of fluids crossing an active area 962,received incoming light from an illumination source within theinstrument, and detect and capture digital images of the fluorescenceemitted from the fluid in connection with a fluidics analysis operation.The analysis circuit 958 includes ports 964 that communicate with theactive area 962 within the analysis circuit 958. The fluids enter theactive area 962 through one of active area ports 964 and the fluid exitsthe active area 962 through the other of the active area ports 964. Theanalysis circuit 958 includes a top surface that is transparent toreceive light that is emitted through the flow cell window 928 (andthrough window 410 of FIG. 4 ). The incoming light illuminates thefluids in the active area 962, and in response thereto, reagents withinthe fluid emitted fluorescence within different fluorescent spectrumsdepending upon the characteristics of the sample. The analysis circuit958 detects the emitted fluorescent spectrums and captures imagesthereof that are then conveyed through the contact pads 950 to theinstrument.

FIG. 9E illustrates a bottom view of the printed circuit board 952 ofFIG. 9D formed in accordance with an example herein. The PCB 952includes a bottom surface 954 that includes the array of contact pads950 visible through the contact pad openings 946. In the presentexample, the array of contact pads 950 are formed in multiple rows.Optionally, alternative contact array configurations may be utilized.The contact pads 950 are connected to corresponding pins within a socketconnector 953. The socket connector 953 includes a plurality of contactpins facing in the direction of the top surface 956 (FIG. 9D). Thesocket connector 953 securely receives the analysis circuit 958 andprovides power, data and communications connections between theinputs/outputs of the analysis circuit 958 and the contact pads 950.

The bottom surface 954 also includes a heat spreader 955 that includes acircuit engaging face (not visible in FIG. 9D) that abuts against abottom surface of the analysis circuit 958. The heat spreader 955includes a heat element engaging face 957 that is oriented to facedownward through the opening 944 in the bottom frame 906 (FIG. 9C).During operation, a heating element on the instrument is inserted intothe opening 944 to abut against the heat element engaging face 957 ofthe heat spreader 955, in connection with providing the desired amountof heat to the analysis circuit 958.

The printed circuit board 952 also includes indents 957 provided about aperimeter thereof. The indents 957 mate with corresponding featureswithin the top and bottom frames 904, 906 to position the printedcircuit board 952 at a particular location within the top and bottomframes 904 and 906.

The top and bottom frames 904 and 906 also include one or moreXY-position features (corresponding to XY-datum points) that areutilized to register the flow cell cartridge 900 in the XY directionwithin the flow cell chamber 108. The XY position features include afront reference post 923 provided on the loading end 908 and one or morelateral reference posts 925 provided along one or both side edges 912. Anotch 927 is provided in a side edge 912 on the side opposite thelateral reference posts 925.

During a loading operation, the loading end 908 is inserted into theflow cell chamber 108 until the reference post 923 firmly abuts againsta limit feature in the flow cell chamber 108 to define a limit ofmovement in the loading direction 9A (also referred to as the Xdirection). As flow cell cartridge 900 is inserted, a biasing arm ridesalong the side edge 912 that includes the notch 927 until a latchelement fits within the notch 927. The latch element is shaped toconform to the shape of the notch 927. The biasing arm applies a lateralforce in the direction of arrow 9C (also represents a lateralpositioning force) to shift the flow cell cartridge 900 in the lateraldirection (corresponding to the Y-axis) until the lateral referenceposts 925 engage mating features within the flow cell chamber 108. Whenthe lateral reference posts 925 engage the mating features, the flowcell chamber 108 defines a limit of movement in the lateral direction9C. The biasing arm maintains the flow cell cartridge 900 at the desiredY-position (corresponding to a Y datum point). The latch element on thebiasing arm fits within the notch 927 at a predefined position tomaintain the flow cell cartridge 900 at the desired X-position(corresponding to an X datum point).

Once the flow cell cartridge 900 is inserted to the XYZ datum points, acommunications connector is inserted (in the Z direction) into thecontact pad openings 946 until a mating array of contacts on thecommunications connector engage the contact pads 950. The communicationsconnector provides power, collects data and controls the operation of,the analysis circuit in the flow cell cartridge 900. In addition, aheating element is inserted (in the Z direction) into the opening 944until engaging the heat spreader 955.

ADDITIONAL EXAMPLES Example 1

A cartridge assembly, comprising: a housing including a flow cellchamber to receive a flow cell; a well plate having liquid wells toreceive desired amounts of liquids, the well plate including a valvestation, a pump station and a fluidics analysis station, the well plateincluding channels associated with the wells, the valve station, pumpstation and fluidics analysis station; a pump assembly provided on thewell plate at the pump station, the pump assembly to manage fluid flowthrough the channels between the pump station and the fluidics analysisstation; and a rotary valve assembly positioned on the well plate at thevalve station, the rotary valve assembly including a rotor shaft androtor valve positioned to rotate about a rotational axis and toselectively couple the wells to the pump station, the rotor shaft havinga distal end exposed through the housing, the rotor shaft including adual spline configuration at the distal end thereof, the dual splineconfiguration having first and second sets of splines, the first set ofsplines forming a drive interface, the second set of splines forming aposition encoding interface.

Example 2

The cartridge assembly of Example 1, wherein the distal end of the rotorshaft extends into a shaft well provided in the housing, therebyexposing the dual spline configuration to a valve drive assembly of afluidics analysis instrument.

Example 3

The cartridge assembly of Example 1, wherein the first set of splinesrepresent exterior splines extending about an exterior of the distalend, wherein lateral sides of adjacent splines are separated by a firstpredetermined spline to spline spacing, the spline to spline spacingcorresponds to a spline pattern on a drive shaft of a valve driveassembly.

Example 4

The cartridge assembly of Example 1, wherein the second set of splinesrepresent interior splines formed about an interior of a cavity providedat the distal end of the rotor shaft, the interior splines havinglateral sides that are angled such that adjacent lateral sides form apredetermined non-parallel angle with respect to one another, whereinthe adjacent lateral sides merge at a bottom to form pockets to receivemating splines on a drive shaft of the valve drive assembly, theposition encoding interface utilized by the valve drive assembly totrack a position of the rotor shaft.

Example 5

The cartridge assembly of Example 1, wherein the rotor valve is mountedto a proximal end of the rotor shaft through a coupling flange, thecoupling flange to allow a predetermined amount of tilting movementbetween the rotor valve and rotor shaft.

Example 6

The cartridge assembly of Example 4, wherein the rotor valve including arotor base having one or more ribs positioned about a proximal end ofthe rotor shaft, the coupling flange held between the ribs and theproximal end of the rotor shaft.

Example 7

The cartridge assembly of Example 1, wherein rotor valve includes wellplate engaging face having a central port and a radial port, the rotorvalve including a channel oriented to extend in a radial directionoutward from the central port to the radial port.

Example 8

The cartridge assembly of Example 6, wherein the central port is alignedto correspond with a rotational axis of the rotor shaft and to alignwith a central feed port in the well plate, the rotor valve to rotateabout the rotational axis to align the radial port with a correspondingwell port.

Example 9

The cartridge assembly of Example 1, wherein the rotary valve includes awell plate engaging face formed with an interface ring thereon, theinterface ring extending about a perimeter of the well plate engagingface.

Example 10

The cartridge assembly of Example 1, further comprising: a valve capincluding an interior cavity to rotatably receive the rotary valve, thevalve cap including one or more latch arms to secure the valve cap tothe wells and downward against the well plate; and a biasing elementprovided within the interior cavity and to apply a biasing force againstthe rotary valve to maintain a sealed interface between ports in therotary valve and ports in the well plate.

Example 11

The cartridge assembly of Example 1, wherein the pump assembly includesa plunger having a drive end and a biasing surface located at oppositeends of the plunger, the drive end and biasing surface exposed at upperand lower surfaces of the housing such that corresponding unidirectionaldrive and biasing forces are applied thereto in connection with movingthe plunger in a reciprocating motion.

Example 12

The cartridge assembly of Example 11, wherein the plunger has a drivearm and a plunger arm joined with one another through a bridge segmentin a U-shape and are formed together in a monolithic structure, thedrive and plunger arms to be received within support posts located onthe well plate.

Example 13

The cartridge assembly of Example 11, wherein the plunger comprises aplunger arm and plunger element that are molded together from differentmaterials.

Example 14

The cartridge assembly of Example 13, wherein the plunger element isformed on a leading end of the plunger arm, the plunger element to movewithin the corresponding support post to form high and low pressurestates at the pumping station.

Example 15

The cartridge assembly of Example 1, wherein the pump station includes achannel segment functionally divided into a preparation segment, adischarge segment and a pump work segment, all of which are formedcontinuous with one another to support fluid flow in either direction.

Example 16

The cartridge assembly of Example 1, wherein the pump station includesan work area sandwiched between a pair of pinch valves located upstreamand downstream of the work area, the pump assembly comprising a plungeraligned with the work area, the plunger to reciprocally move toward andaway from the work area to introduce high and low pressure states, thepump assembly further comprising push pins aligned with the pinchvalves, the push pins to be alternately moved to open and close thepinch valves.

Example 17

The cartridge assembly of Example 1, further comprising a piercer unitprovided in the housing and positioned proximate to the wells, thepiercer unit including a piercer element, the piercer unit to be movedto a piercing position where the piercer element pierces a cover for thecorresponding well.

Example 18

The cartridge assembly of Example 17, wherein the housing includes acover having a piercer access opening that provides an instrument accessto an upper end of the piercer unit.

Example 19

The cartridge assembly of Example 17, wherein the piercer unit includesa body that is shaped in a conical tubular manner with a lower platform,an intermediate segment and an upper flange, at least one of the lowerplatform or upper flange including piercing elements distributed in apredetermined manner, the piercing elements arranged to align with thewells on the well plate.

Example 20

The cartridge assembly of Example 1, further comprising a piercer unithaving a platform that fits over the rotor shaft, the platform includingindexing features that engage mating features on the rotary valveassembly to locate the piercer unit in a predetermined rotationalorientation with respect to the rotor shaft in order to align piercerelements with corresponding wells.

Example 21

The cartridge assembly of Example 1, wherein the well plate includeswell transition ports arranged in a predetermined pattern correspondingto the rotary valve assembly, the well plate including well dischargeports aligned with corresponding wells, the well plate including welldischarge channels extending between corresponding well discharge portsand well transition ports.

Example 22

The cartridge assembly of Example 1, wherein the well plate includes abase having top and bottom surfaces, at least one of which includes thechannels, the channels including open sided channels, the base joined toa backing layer to close the open sided channels.

Example 23

The cartridge assembly of Example 1, wherein the well plate includes anoptical interface window, provided within the optical analysis station,a top side of the well plate including an insertion limit element toengage an illumination element on an instrument.

Example 24

The cartridge assembly of Example 23, wherein the insertion limitelement represents one or more ribs that are provided about the opticalinterface window, the ribs defining a Z-tolerance between anillumination element and the optical interface window.

Example 25

A fluidics system, comprising: a cartridge assembly having a housingthat includes an illumination chamber and a well plate, the well platemaintained within the housing and having liquid wells to receive desiredamounts of liquids, the well plate including a fluidics analysis stationaligned with the illumination chamber, the well plate including aninterface window and interface ports located at the fluidics analysisstation; and a flow cell cartridge having a frame that contains ananalysis circuit therein, the frame including a flow cell window alignedwith the analysis circuit, the frame including flow cell ports that arefluidly coupled to an active area in the analysis circuit, the housingincluding a flow cell chamber to receive the flow cell cartridge, theflow cell chamber to position the flow cell cartridge at the fluidicsanalysis station with the flow cell window and ports aligned with thecorresponding interface window and ports, respectively.

Example 26

The fluidics system of Example 25, wherein the flow cell chamberincludes side rails and an end stop, at least one of which has an endlimit to position the flow cell cartridge, when in a fully loadedposition, at a predetermined datum point such that the flow cell windowand ports aligned with the corresponding interface window and ports,respectively.

Example 27

The fluidic system of Example 26, wherein the flow cell chamber includesa biasing arm that is oriented to extend along at least one of the siderails, the biasing arm extending inward toward the flow cell chamber,the biasing arm to apply a lateral biasing force upon the flow cellcartridge to maintain the flow cell cartridge at the predetermined datumpoint.

Example 28

The fluidic system of Example 27, wherein the biasing arm includes alatch element positioned to fit with a notch provided in a lateral sideof the flow cell cartridge, the latch element to maintain the flow cellcartridge at an X datum point.

Example 29

The fluidic system of Example 25, wherein the flow cell cartridgeincludes top and bottom frames, the top frame including the flow cellwindow and ports, the top frame including a rib extending upward fromthe top frame by a predetermined height to define a Z datum point.

Example 30

The fluidic system of Example 25, wherein the flow cell cartridgeincludes gaskets formed in a monolithic manner from an elastomermaterial.

Example 31

The fluidic system of Example 25, wherein the well plate includes avalve station, pump station and interface channels, the interfacechannels providing a first fluidic path between the valve station andone of the interface ports and a second fluidic path between the pumpstation and one of the interface ports.

Example 32

The fluidic system of Example 25, wherein the illumination chamber isoriented to extend along an illumination axis that extends through theinterface window, flow cell window and the active area within theanalysis circuit.

Closing Statements

It should be appreciated that all combinations of the foregoing concepts(provided such concepts are not mutually inconsistent) are contemplatedas being part of the inventive subject matter disclosed herein. Inparticular, all combinations of aforementioned Examples and claimedsubject matter appearing at the end of this disclosure are contemplatedas being part of the inventive subject matter disclosed herein.

All publications, patents, and patent applications cited in thisSpecification are hereby incorporated by reference in their entirety.

It will be appreciated that various aspects of the present disclosuremay be embodied as a method, system, computer readable medium, and/orcomputer program product. Aspects of the present disclosure may take theform of hardware examples, software examples (including firmware,resident software, micro-code, etc.), or examples combining software andhardware aspects that may all generally be referred to herein as a“circuit,” “module,” or “system.” Furthermore, the methods of thepresent disclosure may take the form of a computer program product on acomputer-usable storage medium having computer-usable program codeembodied in the medium.

Any suitable computer useable medium may be utilized for softwareaspects of the present disclosure. The computer-usable orcomputer-readable medium may be, for example but not limited to, anelectronic, magnetic, optical, electromagnetic, infrared, orsemiconductor system, apparatus, device, or propagation medium. Thecomputer readable medium may include transitory examples. More specificexamples (a non-exhaustive list) of the computer-readable medium wouldinclude some or all of the following: an electrical connection havingone or more wires, a portable computer diskette, a hard disk, a randomaccess memory (RAM), a read-only memory (ROM), an erasable programmableread-only memory (EPROM or Flash memory), an optical fiber, a portablecompact disc read-only memory (CD-ROM), an optical storage device, atransmission medium such as those supporting the Internet or anintranet, or a magnetic storage device. Note that the computer-usable orcomputer-readable medium could even be paper or another suitable mediumupon which the program is printed, as the program can be electronicallycaptured, via, for instance, optical scanning of the paper or othermedium, then compiled, interpreted, or otherwise processed in a suitablemanner, if necessary, and then stored in a computer memory. In thecontext of this document, a computer-usable or computer-readable mediummay be any medium that can contain, store, communicate, propagate, ortransport the program for use by or in connection with the instructionexecution system, apparatus, or device.

Program code for carrying out operations of the methods and apparatusset forth herein may be written in an object oriented programminglanguage such as Java, Smalltalk, C++ or the like. However, the programcode for carrying out operations of the methods and apparatus set forthherein may also be written in conventional procedural programminglanguages, such as the “C” programming language or similar programminglanguages. The program code may be executed by a processor, applicationspecific integrated circuit (ASIC), or other component that executes theprogram code. The program code may be simply referred to as a softwareapplication that is stored in memory (such as the computer readablemedium discussed above). The program code may cause the processor (orany processor-controlled device) to produce a graphical user interface(“GUI”). The graphical user interface may be visually produced on adisplay device, yet the graphical user interface may also have audiblefeatures. The program code, however, may operate in anyprocessor-controlled device, such as a computer, server, personaldigital assistant, phone, television, or any processor-controlled deviceutilizing the processor and/or a digital signal processor.

The program code may locally and/or remotely execute. The program code,for example, may be entirely or partially stored in local memory of theprocessor-controlled device. The program code, however, may also be atleast partially remotely stored, accessed, and downloaded to theprocessor-controlled device. A user's computer, for example, mayentirely execute the program code or only partly execute the programcode. The program code may be a stand-alone software package that is atleast partly on the user's computer and/or partly executed on a remotecomputer or entirely on a remote computer or server. In the latterscenario, the remote computer may be connected to the user's computerthrough a communications network.

The methods and apparatus set forth herein may be applied regardless ofnetworking environment. The communications network may be a cablenetwork operating in the radial-frequency domain and/or the InternetProtocol (IP) domain. The communications network, however, may alsoinclude a distributed computing network, such as the Internet (sometimesalternatively known as the “World Wide Web”), an intranet, a local-areanetwork (LAN), and/or a wide-area network (WAN). The communicationsnetwork may include coaxial cables, copper wires, fiber optic lines,and/or hybrid-coaxial lines. The communications network may even includewireless portions utilizing any portion of the electromagnetic spectrumand any signaling standard (such as the IEEE 802 family of standards,GSM/CDMA/TDMA or any cellular standard, and/or the ISM band). Thecommunications network may even include powerline portions, in whichsignals are communicated via electrical wiring. The methods andapparatus set forth herein may be applied to any wireless/wirelinecommunications network, regardless of physical componentry, physicalconfiguration, or communications standard(s).

Certain aspects of present disclosure are described with reference tovarious methods and method steps. It will be understood that each methodstep can be implemented by the program code and/or by machineinstructions. The program code and/or the machine instructions maycreate means for implementing the functions/acts specified in themethods.

The program code may also be stored in a computer-readable memory thatcan direct the processor, computer, or other programmable dataprocessing apparatus to function in a particular manner, such that theprogram code stored in the computer-readable memory produce or transforman article of manufacture including instruction means which implementvarious aspects of the method steps.

The program code may also be loaded onto a computer or otherprogrammable data processing apparatus to cause a series of operationalsteps to be performed to produce a processor/computer implementedprocess such that the program code provides steps for implementingvarious functions/acts specified in the methods of the presentdisclosure.

What is claimed is:
 1. An apparatus, comprising: a cartridge assembly,comprising: a housing comprising an instrument engaging surface definingan opening, a front face that includes a flow cell chamber, and aperipheral wall that forms an illumination chamber; a well platecomprising wells and a fluidics analysis station; and a rotary valveassembly rotatably mounted on the well plate, the opening providingaccess to the rotary valve assembly.
 2. The apparatus of claim 1,wherein the wells each have a filling end, further comprising a covercovering the filling ends of the wells.
 3. The apparatus of claim 2,further comprising a piercing unit within the housing and positionedproximate the wells.
 4. The apparatus of claim 3, wherein the piercingunit comprises piercing elements arranged in a circular pattern.
 5. Theapparatus of claim 3, wherein the instrument engaging surface comprisespiercer access openings.
 6. The apparatus of claim 1, wherein the rotaryvalve assembly selectively couples the wells to the fluidics analysisstation.
 7. The apparatus of claim 1, further comprising a sample welland wherein the cartridge assembly comprises a heating element proximateto the sample well.
 8. The apparatus of claim 1, wherein the rotaryvalve assembly selectively couples the wells to the fluidics analysisstation.
 9. The apparatus of claim 1, further comprising a flow cellcartridge receivable within the flow cell chamber.
 10. The apparatus ofclaim 9, wherein a snap-in arrangement is provided between the flow cellchamber and the flow cell cartridge when the flow cell cartridge isreceived within the flow cell chamber.
 11. The apparatus of claim 1,further comprising a syringe pump assembly mounted onto the well plate.12. The apparatus of claim 11, wherein the syringe pump assembly and therotary valve assembly control flow from the corresponding wells to thefluidics analysis station.
 13. The apparatus of claim 1, wherein thewell plate comprises a mating surface, further comprising a waste traycomprising a ridge that is sealed to the mating surface of the wellplate.
 14. The apparatus of claim 13, wherein the ridge comprises avent.
 15. The apparatus of claim 1, wherein the flow cell chambercomprises a key feature comprising a channel.
 16. The apparatus of claim1, further comprising reagent contained within the wells.
 17. Theapparatus of claim 1, wherein the well plate comprises a valve station,a pump station, ports, and channels, the channels providing a firstfluidic path between the valve station and one of the ports and a secondfluidic path between the pump station and one of the ports.
 18. Theapparatus of claim 1, wherein the well plate comprises an opticalinterface window, channels, and ports that correspond to the channelspositioned proximate the optical interface window.
 19. The apparatus ofclaim 18, wherein the illumination chamber extends along an illuminationaxis that extends through the optical interface window.
 20. Theapparatus of claim 19, further comprising a flow cell cartridgereceivable within the flow cell chamber, the flow cell cartridgecomprises a flow cell window and an analysis circuit comprising anactive area and active area ports that communicate with the active area,the active area ports to commute with the ports of the well plate whenthe flow cell cartridge is received within the flow cell chamber and theillumination axis extends through the flow cell window and the activearea when the flow cell cartridge is received within the flow cellchamber.
 21. A fluidics system, comprising: a cartridge assembly havinga housing that includes an illumination chamber and a well plate, thewell plate maintained within the housing and having liquid wells toreceive desired amounts of liquids, the well plate including a fluidicsanalysis station aligned with the illumination chamber, the well plateincluding an interface window and interface ports located at thefluidics analysis station; and a flow cell cartridge having a frame thatcontains an analysis circuit therein, the frame including a flow cellwindow aligned with the analysis circuit, the frame including flow cellports that are fluidly coupled to an active area in the analysiscircuit, the housing including a flow cell chamber to receive the flowcell cartridge, the flow cell chamber to position the flow cellcartridge at the fluidics analysis station with the flow cell window andports aligned with the corresponding interface window and ports,respectively.
 22. The fluidics system of claim 21, wherein the flow cellchamber includes side rails and an end stop, at least one of which hasan end limit to position the flow cell cartridge, when in a fully loadedposition, at a predetermined datum point such that the flow cell windowand ports aligned with the corresponding interface window and ports,respectively.
 23. The fluidics system of claim 22, wherein the flow cellchamber includes a biasing arm that is oriented to extend along at leastone of the side rails, the biasing arm extending inward toward the flowcell chamber, the biasing arm to apply a lateral biasing force upon theflow cell cartridge to maintain the flow cell cartridge at thepredetermined datum point.
 24. The fluidics system of claim 23, whereinthe biasing arm includes a latch element positioned to fit with a notchprovided in a lateral side of the flow cell cartridge, the latch elementto maintain the flow cell cartridge at an X datum point.
 25. Thefluidics system of claim 21, wherein the flow cell cartridge includestop and bottom frames, the top frame including the flow cell window andports, the top frame including a rib extending upward from the top frameby a predetermined height to define a Z datum point.
 26. The fluidicssystem of claim 21, wherein the flow cell cartridge includes gasketsformed in a monolithic manner from an elastomer material.
 27. Thefluidics system of claim 21, wherein the well plate includes a valvestation, a pump station, and interface channels, the interface channelsproviding a first fluidic path between the valve station and one of theinterface ports and a second fluidic path between the pump station andone of the interface ports.
 28. The fluidics system of claim 21, whereinthe illumination chamber is oriented to extend along an illuminationaxis that extends through the interface window, flow cell window and theactive area within the analysis circuit.